Puno (C.J., Chairperson), Carpio-Morales, Leonardo-De Castro Petition Denied, Judgment Affirmed

2/6/2019 SUPREME COURT REPORTS ANNOTATED VOLUME 614
cular person does not foreclose the possibility that the real
property may be co-owned with persons not named in the
certificate, or that it may be held in trust for another
person by the registered owner.25
WHEREFORE, the petition for review on certiorari is
denied, and the decision dated January 28, 2002 is
affirmed.
The petitioners are ordered to pay the costs of suit.
SO ORDERED.
Puno (C.J., Chairperson), Carpio-Morales, Leonardo-

De Castro and Villarama, Jr., JJ., concur.
Petition denied, judgment affirmed.
Note.—Prescription does not run against the

government. (Land Bank of the Philippines vs. Republic,
542 SCRA 453 [2008])
——o0o——
G.R. No. 157594. March 9, 2010.*
TOSHIBA INFORMATION EQUIPMENT (PHILS.), INC.,

petitioner, vs. COMMISSIONER OF INTERNAL
REVENUE, respondent.
Remedial Law; Pleadings and Practice; It is axiomatic in

pleadings and practice that no new issue in a case can be raised in
a pleading which by due diligence could have been raised in
previous pleadings; The first and fundamental concern of the rules
of procedure is to secure a just determination of every action.—It is
axiomatic
_______________
25 Heirs of Clemente Ermac v. Heirs of Vicente Ermac, G.R. No. 149679, May
30, 2003, 403 SCRA 291, 298.
* FIRST DIVISION.
527
VOL. 614, March 9, 2010 527

http://central.com.ph/sfsreader/session/00000168c0616a895e8477aa003600fb002c009e/t/?o=False 1/37
Toshiba Information Equipment (Phils.), Inc. vs. Commissioner of

Internal Revenue
in pleadings and practice that no new issue in a case can be raised

in a pleading which by due diligence could have been raised in
previous pleadings. The Court cannot simply grant the plea of the
CIR that the procedural rules be relaxed based on the general
averment of the interest of substantive justice. It should not be
forgotten that the first and fundamental concern of the rules of
procedure is to secure a just determination of every action.
Procedural rules are designed to facilitate the adjudication of
cases. Courts and litigants alike are enjoined to abide strictly by
the rules. While in certain instances, the Court allows a
relaxation in the application of the rules, it never intends to forge
a weapon for erring litigants to violate the rules with impunity.
The liberal interpretation and application of rules apply only in
proper cases of demonstrable merit and under justifiable causes
and circumstances.
Same; Same; Pre-trial; Pre-trial is an answer to the clarion
call for the speedy disposition of cases; It was made mandatory
under the 1964 Rules and the subsequent amendments in 1997.—
Pre-trial is an answer to the clarion call for the speedy disposition
of cases. Although it was discretionary under the 1940 Rules of
Court, it was made mandatory under the 1964 Rules and the
subsequent amendments in 1997. It has been hailed as “the most
important procedural innovation in Anglo-Saxon justice in the
nineteenth century.”
Same; Same; Same; Admission; The admission having been
made in a stipulation of facts at pre-trial by the parties, it must be
treated as a judicial admission; An admission made by a party in
the course of the proceedings does not require proof.—The
admission having been made in a stipulation of facts at pre-trial
by the parties, it must be treated as a judicial admission. Under
Section 4, Rule 129 of the Rules of Court, a judicial admission
requires no proof. The admission may be contradicted only by a
showing that it was made through palpable mistake or that no
such admission was made. The Court cannot lightly set aside a
judicial admission especially when the opposing party relied upon
the same and accordingly dispensed with further proof of the fact
already admitted. An admission made by a party in the course of
the proceedings does not require proof.
PETITION for review on certiorari of a decision of the

Court of Appeals.
The facts are stated in the opinion of the Court.
528
528 SUPREME COURT REPORTS ANNOTATED

Toshiba Information Equipment (Phils.), Inc. vs.
Commissioner of Internal Revenue
Agan & Montenegro Law Offices for petitioner.

The Solicitor General for respondent.
LEONARDO-DE CASTRO, J.:

In this Petition for Review on Certiorari1 under Rule 45
of the Rules of Court, petitioner Toshiba Information
Equipment (Philippines), Inc. (Toshiba) seeks the reversal
and setting aside of (1) the Decision2 dated August 29, 2002
of the Court of Appeals in CA-G.R. SP No. 63047, which
found that Toshiba was not entitled to the credit/refund of
its unutilized input Value-Added Tax (VAT) payments
attributable to its export sales, because it was a tax-exempt
entity and its export sales were VAT-exempt transactions;
and (2) the Resolution3 dated February 19, 2003 of the
appellate court in the same case, which denied the Motion
for Reconsideration of Toshiba. The herein assailed
judgment of the Court of Appeals reversed and set aside
the Decision4 dated October 16, 2000 of the Court of Tax
Appeals (CTA) in CTA Case No. 5762 granting the claim
for credit/refund of Toshiba in the amount of P1,385,282.08.
Toshiba is a domestic corporation principally engaged in
the business of manufacturing and exporting of electric
machinery, equipment systems, accessories, parts,
components, materials and goods of all kinds, including
those relating to office automation and information
technology and all types of computer hardware and
software, such as but not limited to
_______________
1 Rollo, pp. 11-32.

2 Penned by Associate Justice Rodrigo V. Cosico with Associate
Justices Buenaventura J. Guerrero and Perlita J. Tria-Tirona, concurring;
Rollo, pp. 35- 52.
3 Id., at pp. 54-55.
4 Penned by Associate Judge Amancio Q. Saga with Presiding Judge
Ernesto D. Acosta and Associate Judge Ramon O. De Veyra, concurring;
Rollo, pp. 83-92.
529
VOL. 614, March 9, 2010 529

HDD-CD-ROM and personal computer printed circuit

board.5 It is registered with the Philippine Economic Zone
Authority (PEZA) as an Economic Zone (ECOZONE) export
enterprise in the Laguna Technopark, Inc., as evidenced by
Certificate of Registration No. 95-99 dated September 27,
1995.6 It is also registered with Regional District Office No.
57 of the Bureau of Internal Revenue (BIR) in San Pedro,
Laguna, as a VAT-taxpayer with Taxpayer Identification
No. (TIN) 004-739-137.7
In its VAT returns for the first and second quarters of
1997,8 filed on April 14, 1997 and July 21, 1997,
respectively, Toshiba declared input VAT payments on its
domestic purchases of taxable goods and services in the
aggregate sum of P3,875,139.65,9 with no zero-rated sales.
Toshiba subsequently submitted to the BIR on July 23,
1997 its amended VAT returns for the first and second
quarters of 1997,10 reporting the same amount of input
VAT payments but, this time, with zero-rated sales totaling
P7,494,677,000.00.11
On March 30, 1999, Toshiba filed with the One-Stop
Shop Inter-Agency Tax Credit and Duty Drawback Center
of the Department of Finance (DOF One-Stop Shop) two
separate applications for tax credit/refund12 of its
unutilized input VAT payments for the first half of 1997 in
the total amount of P3,685,446.73.13
_______________
5 Rollo, p. 12.
6 Exhibit “A,” Folder of Exhibits “A-I” of Toshiba.
7 Records, p. 7.
8 Exhibits “B” and “C,” Folder of Exhibits “A-I” of Toshiba.
9 Toshiba declared P3,320,034.44 and P555,105.21 of input VAT
payments for the first and second quarters or 1997, respectively.
10 Exhibits “B-1” and “C-1,” Folder of Exhibits “A-I” of Toshiba.
11 Toshiba reported P2,083,305,000.00 and P5,411,372,000.00 of zero-
rated sales for the first and second quarters of 1997, respectively.
12 Records, pp. 10-13.
13 Toshiba claimed in its applications for refund/credit P3,268,682.34
and P416,764.39 of local input VAT for the first and second quarters of
1997, respectively.
530

The next day, on March 31, 1999, Toshiba likewise filed

with the CTA a Petition for Review14 to toll the running of
the two-year prescriptive period under Section 230 of the
Tax Code of 1977,15 as amended.16 In said Petition,
docketed as CTA Case No. 5762, Toshiba prayed that—
“[A]fter due hearing, judgment be rendered ordering [herein

respondent Commissioner of Internal Revenue (CIR)] to refund or
issue to [Toshiba] a tax refund/tax credit certificate in the amount
of P3,875,139.65 representing unutilized input taxes paid on its
pur-
_______________

15 Republic Act No. 8424, otherwise known as the Tax Code of 1997, took effect
only on January 1, 1998. Prior to said date, Presidential Decree No. 1158,
otherwise known as the Tax Code of 1977, as amended, was in effect. According to
Section 230 of the Tax Code of 1977, as amended:
Sec. 230. Recovery of tax erroneously or illegally collected.—No suit or
proceeding shall be maintained in any court for the recovery of any
national internal revenue tax hereafter alleged to have been erroneously or
illegally assessed or collected, or of any penalty claimed to have been
collected without authority, or of any sum alleged to have been excessive or
in any manner wrongfully collected, until a claim for refund or credit has
been duly filed with the Commissioner; but such suit or proceeding may be
maintained, whether or not such tax, penalty, or sum has been paid under
protest or duress.
In any case, no such suit or proceeding shall be begun after the
expiration of two years from the date of payment of the tax or
penalty regardless of any supervening cause that may arise after
payment: Provided, however, That the Commissioner may, even without a
written claim therefor, refund or credit any tax, where on the face of the
return upon which payment was made, such payment appears clearly to
have been erroneously paid. (Emphasis ours.)
16 As amended by Republic Act No. 7716, bearing the title “An Act
Restructuring the Value Added Tax (VAT) System, Widening its Tax Base and
Enhancing its Administration and for These Purposes Amending and Repealing
the Relevant Provisions of the National Internal Revenue Code, As Amended, and
For Other Purposes.”
531
VOL. 614, March 9, 2010 531

Internal Revenue
chase of taxable goods and services for the period January 1 to

June 30, 1997.”17
The Commissioner of Internal Revenue (CIR) opposed

the claim for tax refund/credit of Toshiba, setting up the
following special and affirmative defenses in his Answer18
—
5. [Toshiba’s] alleged claim for refund/tax credit is subject to

administrative routinary investigation/examination by [CIR’s]
Bureau;
6. [Toshiba] failed miserably to show that the total amount of
P3,875,139.65 claimed as VAT input taxes, were erroneously or
illegally collected, or that the same are properly documented;
7. Taxes paid and collected are presumed to have been made
in accordance with law; hence, not refundable;
8. In an action for tax refund, the burden is on the taxpayer
to establish its right to refund, and failure to sustain the burden
is fatal to the claim for refund;
9. It is incumbent upon [Toshiba] to show that it has complied
with the provisions of Section 204 in relation to Section 229 of the
Tax Code;
10. Well-established is the rule that claims for refund/tax
credit are construed in strictissimi juris against the taxpayer as it
partakes the nature of exemption from tax.19
Upon being advised by the CTA,20 Toshiba and the CIR

filed a Joint Stipulation of Facts and Issues,21 wherein the
opposing parties “agreed and admitted” that—
1. [Toshiba] is a duly registered value-added tax entity in

accordance with Section 107 of the Tax Code, as amended.
_______________
17 Records, p. 5.
18 Id., at pp. 20-22.
19 Id., at p. 21.
20 Id., at p. 33.
21 Id., at pp. 34-35.
532

Internal Revenue
2. [Toshiba] is subject to zero percent (0%) value-added tax on

its export sales in accordance with then Section 100(a)(2)(A) of the
Tax Code, as amended.
3. [Toshiba] filed its quarterly VAT returns for the first two
quarters of 1997 within the legally prescribed period.
xxxx
7. [Toshiba] is subject to zero percent (0%) value-added tax

on its export sales.
8. [Toshiba] has duly filed the instant Petition for Review
within the two-year prescriptive period prescribed by then Section
230 of the Tax Code.22
In the same pleading, Toshiba and the CIR jointly

submitted the following issues for determination by the
CTA—
Whether or not [Toshiba] has incurred input taxes in the amount

of P3,875,139.65 for the period January 1 to June 30, 1997 which
are directly attributable to its export sales[.]
Whether or not the input taxes incurred by [Toshiba] for the
period January 1 to June 30, 1997 have not been carried over to
the succeeding quarters[.]
Whether or not input taxes incurred by [Toshiba] for the first two
quarters of 1997 have not been offset against any output tax[.]
Whether or not input taxes incurred by [Toshiba] for the first two
quarters of 1997 are properly substantiated by official receipts
and invoices.23
During the trial before the CTA, Toshiba presented

documentary evidence in support of its claim for tax
credit/refund, while the CIR did not present any evidence
at all.
With both parties waiving the right to submit their
respective memoranda, the CTA rendered its Decision in
CTA Case No. 5762 on October 16, 2000 favoring Toshiba.
According to the CTA, the CIR himself admitted that the
export sales of
_______________
22 Id.
23 Id., at p. 35.
533
VOL. 614, March 9, 2010 533

Toshiba were subject to zero percent (0%) VAT based on

Section 100(a)(2)(A)(i) of the Tax Code of 1977, as amended.
Toshiba could then claim tax credit or refund of input VAT
paid on its purchases of goods, properties, or services,
directly attributable to such zero-rated sales, in accordance
with Section 4.102-2 of Revenue Regulations No. 7-95. The
CTA, though, reduced the amount to be credited or

refunded to Toshiba to P1,385,292.02.
The dispositive portion of the October 16, 2000 Decision
of the CTA fully reads—
“WHEREFORE, [Toshiba’s] claim for refund of unutilized

input VAT payments is hereby GRANTED but in a reduced
amount of P1,385,282.08 computed as follows:
1st Quarter 2nd Total

Quarter

Amount of claimed
input taxes filed with
the DOF One Stop P3,268,682.34 P416,764.39 P3,685,446.73
Shop Center
Less: 1)
Input taxes not
properly
supported by
VAT invoices
and official
receipts
a. Per SGV’s
verification
(Exh. I) P 242,491.45 P154,391.13 P 396,882.58

b. Per this
court’s further
verification P1,852,437.65 P35,108.00 P1,887,545.65
(Annex A)
2) 1998 4th
qtr. Output
VAT Liability
applied against
the claimed 15,736.42
input taxes 15,736.42

Subtotal
P2,110,665.52 P189,499.13 P2,300,164.65

Amount Refundable P1,158,016.82 P227,265.26 P1,385,282.08

Respondent Commissioner of Internal Revenue is ORDERED

to REFUND to [Toshiba] or in the alternative, ISSUE a TAX
CREDIT CERTIFICATE in the amount of P1,385,282.08
representing unutilized input taxes paid by [Toshiba] on its
purchases of taxable goods and services for the period January 1
to June 30, 1997.”24
_______________
24 Id., at pp. 91-92.
534

Both Toshiba and the CIR sought reconsideration of the

foregoing CTA Decision.
Toshiba asserted in its Motion for Reconsideration25 that
it had presented proper substantiation for the
P1,887,545.65 input VAT disallowed by the CTA.The CIR,
on the other hand, argued in his Motion for
Reconsideration26 that Toshiba was not entitled to the
credit/refund of its input VAT payments because as a
PEZA-registered ECOZONE export enterprise, Toshiba
was not subject to VAT. The CIR invoked the following
statutory and regulatory provisions—
Section 24 of Republic Act No. 791627

SECTION 24. Exemption from Taxes Under the National
Internal Revenue Code.—Any provision of existing laws, rules and
regulations to the contrary notwithstanding, no taxes, local and
national, shall be imposed on business establishments operating
within the ECOZONE. In lieu of paying taxes, five percent (5%) of
the gross income earned by all businesses and enterprises within
the ECOZONE shall be remitted to the national government. x x
x.
Section 103(q) of the Tax Code of 1977, as amended
Sec. 103. Exempt transactions.—The following shall be
exempt from the value-added tax:
xxxx
(q) Transactions which are exempt under special laws, except
those granted under Presidential Decree Nos. 66, 529, 972, 1491,
and 1950, and non-electric cooperatives under Republic Act No.
6938, or international agreements to which the Philippines is a
signatory.
_______________
25 Id., at pp. 99-100.

26 Id., at pp. 89-95.
27 Otherwise known as The Special Economic Zone Act of 1995, as amended by
Republic Act No. 8748.
535
VOL. 614, March 9, 2010 535

Internal Revenue
Section 4.103-1 of Revenue Regulations No. 7-95

SEC. 4.103-1. Exemptions.—(A) In general.—An exemption
means that the sale of goods or properties and/or services and the
use or lease of properties is not subject to VAT (output tax) and
the seller is not allowed any tax credit on VAT (input tax)
previously paid.
The person making the exempt sale of goods, properties or
services shall not bill any output tax to his customers because the
said transaction is not subject to VAT. On the other hand, a VAT-
registered purchaser of VAT-exempt goods, properties or services
which are exempt from VAT is not entitled to any input tax on
such purchase despite the issuance of a VAT invoice or receipt.”
The CIR contended that under Section 24 of Republic

Act No. 7916, a special law, all businesses and
establishments within the ECOZONE were to remit to the
government five percent (5%) of their gross income earned
within the zone, in lieu of all taxes, including VAT. This
placed Toshiba within the ambit of Section 103(q) of the
Tax Code of 1977, as amended, which exempted from VAT
the transactions that were exempted under special laws.
Following Section 4.103-1(A) of Revenue Regulations No. 7-
95, the VAT-exemption of Toshiba meant that its sale of
goods was not subject to output VAT and Toshiba as seller
was not allowed any tax credit on the input VAT it had
previously paid.
On January 17, 2001, the CTA issued a Resolution28
denying both Motions for Reconsideration of Toshiba and
the CIR.
The CTA took note that the pieces of evidence referred
to by Toshiba in its Motion for Reconsideration were
insufficient substantiation, being mere schedules of input
VAT payments it had purportedly paid for the first and
second quarters of 1997. While the CTA gives credence to
the report of its commissioned certified public accountant
(CPA), it does not ren-
_______________
28 Signed by Presiding Judge Ernesto D. Acosta and Associate Judges

Amancio Q. Saga and Ramon O. de Veyra. Rollo, pp. 103-106.
536

der its decision based on the findings of the said CPA alone.
The CTA has its own CPA and the tax court itself conducts
an investigation/examination of the documents presented.
The CTA stood by its earlier disallowance of the amount of
P1,887,545.65 as tax credit/refund because it was not
supported by VAT invoices and/or official receipts.
The CTA refused to consider the argument that Toshiba
was not entitled to a tax credit/refund under Section 24 of
Republic Act No. 7916 because it was only raised by the
CIR for the first time in his Motion for Reconsideration.
Also, contrary to the assertions of the CIR, the CTA held
that Section 23, and not Section 24, of Republic Act No.
7916, applied to Toshiba. According to Section 23 of
Republic Act No. 7916—
“SECTION 23. Fiscal Incentives.—Business establishments

operating within the ECOZONES shall be entitled to the fiscal
incentives as provided for under Presidential Decree No. 66, the
law creating the Export Processing Zone Authority, or those
provided under Book VI of Executive Order No. 226, otherwise
known as the Omnibus Investment Code of 1987.
Furthermore, tax credits for exporters using local materials as
inputs shall enjoy the benefits provided for in the Export
Development Act of 1994.”
Among the fiscal incentives granted to PEZA-registered

enterprises by the Omnibus Investments Code of 1987 was
the income tax holiday, to wit—
“Art. 39. Incentives to Registered Enterprises.—All registered

enterprises shall be granted the following incentives to the extent
engaged in a preferred area of investment:
(a) Income Tax Holiday.—
(1) For six (6) years from commercial operation for pioneer
firms and four (4) years for non-pioneer firms, new registered
firms shall be fully exempt from income taxes levied by the
national government. Subject to such guidelines as may be
prescribed by the
537
VOL. 614, March 9, 2010 537

Internal Revenue
Board, the income tax exemption will be extended for another

year in each of the following cases:
(i) The project meets the prescribed ratio of capital equipment

to number of workers set by the Board;
(ii) Utilization of indigenous raw materials at rates set by the
Board;
(iii) The net foreign exchange savings or earnings amount to
at least US$500,000.00 annually during the first three (3) years of
operation.
The preceding paragraph notwithstanding, no registered
pioneer firm may avail of this incentive for a period exceeding
eight (8) years.
(2) For a period of three (3) years from commercial operation,
registered expanding firms shall be entitled to an exemption from
income taxes levied by the National Government proportionate to
their expansion under such terms and conditions as the Board
may determine: Provided, however, That during the period within
which this incentive is availed of by the expanding firm it shall
not be entitled to additional deduction for incremental labor
expense.
(3) The provision of Article 7(14) notwithstanding, registered
firms shall not be entitled to any extension of this incentive.”
The CTA pointed out that Toshiba availed itself of the

income tax holiday under the Omnibus Investments Code
of 1987, so Toshiba was exempt only from income tax but
not from other taxes such as VAT. As a result, Toshiba was
liable for output VAT on its export sales, but at zero
percent (0%) rate, and entitled to the credit/refund of the
input VAT paid on its purchases of goods and services
relative to such zero-rated export sales.
Unsatisfied, the CIR filed a Petition for Review29 with
the Court of Appeals, docketed as CA-G.R. SP No. 63047.
In its Decision dated August 29, 2002, the Court of
Appeals granted the appeal of the CIR, and reversed and
set aside the
_______________
29 Rollo, pp. 107-118.
538

Decision dated October 16, 2000 and the Resolution dated

January 17, 2001 of the CTA. The appellate court ruled
that Toshiba was not entitled to the refund of its alleged
unused input VAT payments because it was a tax-exempt

entity under Section 24 of Republic Act No. 7916. As a
PEZA-registered corporation, Toshiba was liable for
remitting to the national government the five percent (5%)
preferential rate on its gross income earned within the
ECOZONE, in lieu of all other national and local taxes,
including VAT.
The Court of Appeals further adjudged that the export
sales of Toshiba were VAT-exempt, not zero-rated,
transactions. The appellate court found that the Answer
filed by the CIR in CTA Case No. 5762 did not contain any
admission that the export sales of Toshiba were zero-rated
transactions under Section 100(a)(2)(A) of the Tax Code of
1977, as amended. At the least, what was admitted by the
CIR in said Answer was that the Tax Code provisions cited
in the Petition for Review of Toshiba in CTA Case No. 5762
were correct. As to the Joint Stipulation of Facts and Issues
filed by the parties in CTA Case No. 5762, which stated
that Toshiba was subject to zero percent (0%) VAT on its
export sales, the appellate court declared that the CIR
signed the said pleading through palpable mistake. This
palpable mistake in the stipulation of facts should not be
taken against the CIR, for to do otherwise would result in
suppressing the truth through falsehood. In addition, the
State could not be put in estoppel by the mistakes or errors
of its officials or agents.
Given that Toshiba was a tax-exempt entity under
Republic Act No. 7916, a special law, the Court of Appeals
concluded that the export sales of Toshiba were VAT-
exempt transactions under Section 109(q) of the Tax Code
of 1997, formerly Section 103(q) of the Tax Code of 1977.
Therefore, Toshiba could not claim refund of its input VAT
payments on its domestic purchases of goods and services.
The Court of Appeals decreed at the end of its August
29, 2002 Decision—
539
VOL. 614, March 9, 2010 539

“WHEREFORE, premises considered, the appealed decision of

the Court of Tax Appeals in CTA Case No. 5762, is hereby
REVERSED and SET ASIDE, and a new one is hereby rendered
finding [Toshiba], being a tax exempt entity under R.A. No. 7916,
not entitled to refund the VAT payments made in its domestic
purchases of goods and services.30
Toshiba filed a Motion for Reconsideration31 of the

aforementioned Decision, anchored on the following
arguments: (a) the CIR never raised as an issue before the
CTA that Toshiba was tax-exempt under Section 24 of
Republic Act No. 7916; (b) Section 24 of Republic Act No.
7916, subjecting the gross income earned by a PEZA-
registered enterprise within the ECOZONE to a
preferential rate of five percent (5%), in lieu of all taxes, did
not apply to Toshiba, which availed itself of the income tax
holiday under Section 23 of the same statute; (c) the
conclusion of the CTA that the export sales of Toshiba were
zero-rated was supported by substantial evidence, other
than the admission of the CIR in the Joint Stipulation of
Facts and Issues; and (d) the judgment of the CTA granting
the refund of the input VAT payments was supported by
substantial evidence and should not have been set aside by
the Court of Appeals.
In a Resolution dated February 19, 2003, the Court of
Appeals denied the Motion for Reconsideration of Toshiba
since the arguments presented therein were mere
reiterations of those already passed upon and found to be
without merit by the appellate court in its earlier Decision.
The Court of Appeals, however, mentioned that it was
incorrect for Toshiba to say that the issue of the
applicability of Section 24 of Republic Act No. 7916 was
only raised for the first time on appeal before the appellate
court. The said issue was adequately raised by the CIR in
his Motion for Reconsideration before the CTA, and was
even ruled upon by the tax court.
_______________
30 Id., at p. 52.
31 Id., at pp. 147-163.
540

Hence, Toshiba filed the instant Petition for Review

with the following assignment of errors—
5.1 THE HONORABLE COURT OF APPEALS ERRED

WHEN IT RULED THAT [TOSHIBA], BEING A PEZA-
REGISTERED ENTERPRISE, IS EXEMPT FROM VAT UNDER
SECTION 24 OF R.A. 7916, AND FURTHER HOLDING THAT
[TOSHIBA’S] EXPORT SALES ARE EXEMPT TRANSACTIONS

UNDER SECTION 109 OF THE TAX CODE.
WHEN IT FAILED TO DISMISS OUTRIGHT AND GAVE DUE
COURSE TO [CIR’S] PETITION NOTWITHSTANDING [CIR’S]
FAILURE TO ADEQUATELY RAISE IN ISSUE DURING THE
TRIAL IN THE COURT OF TAX APPEALS THE
APPLICABILITY OF SECTION 24 OF R.A. 7916 TO
[TOSHIBA’S] CLAIM FOR REFUND.
WHEN [IT] RULED THAT THE COURT OF TAX APPEALS’
FINDINGS, WITH REGARD [TOSHIBA’S] EXPORT SALES
BEING ZERO RATED SALES FOR VAT PURPOSES, WERE
BASED MERELY ON THE ADMISSIONS MADE BY [CIR’S]
COUNSEL AND NOT SUPPORTED BY SUBSTANTIAL
EVIDENCE.
WHEN IT REVERSED THE DECISION OF THE COURT OF
TAX APPEALS GRANTING [TOSHIBA’S] CLAIM FOR
REFUND[;]32
and the following prayer—
“WHEREFORE, premises considered, Petitioner TOSHIBA

INFORMATION EQUIPMENT (PHILS.), INC. most respectfully
prays that the decision and resolution of the Honorable Court of
Appeals, reversing the decision of the CTA in CTA Case No. 5762,
be set aside and further prays that a new one be rendered
AFFIRMING AND UPHOLDING the Decision of the CTA
promulgated on October 16, 2000 in CTA Case No. 5762.
Other reliefs, which the Honorable Court may deem just and
equitable under the circumstances, are likewise prayed for.”33
_______________
32 Id., at pp. 17-18.

33 Id., at p. 30.
541
VOL. 614, March 9, 2010 541

The Petition is impressed with merit.

The CIR did not timely raise before
the CTA the issues on the VAT-
exemptions of Toshiba and its export

sales.
Upon the failure of the CIR to timely plead and prove
before the CTA the defenses or objections that Toshiba was
VAT-exempt under Section 24 of Republic Act No. 7916,
and that its export sales were VAT-exempt transactions
under Section 103(q) of the Tax Code of 1977, as amended,
the CIR is deemed to have waived the same.
During the pendency of CTA Case No. 5762, the
proceedings before the CTA were governed by the Rules of
the Court of Tax Appeals,34 while the Rules of Court were
applied suppletorily.35
_______________
34 The RCTA was promulgated on September 10, 1955, following the
enactment on June 16, 1954 of Republic Act No. 1125, otherwise known as
An Act Creating the Court of Appeals. Republic Act No. 9282, which was
enacted on March 30, 2004, amended Republic Act No. 1125 by expanding
the jurisdiction of the CTA, elevating the same to the level of a collegiate
court with special jurisdiction, and enlarging its membership. Accordingly,
the Court approved on November 25, 2005 the Revised Rules of the Court
of Tax Appeals (RRCTA). Thereafter, Republic Act No. 9503, which was
enacted on June 12, 2008, further amended Republic Act No. 1125 by
enlarging the organization structure of the CTA. As a result, the Court
approved on September 16, 2008 the amendments to the 2005 RRCTA.
35 Rule 16 of the RCTA is reproduced in full below:
RULE 16
APPLICABILITY OF THE RULES OF THE COURT OF FIRST
INSTANCE
SECTION 1. The provisions of the Rules of Court applicable
to proceedings before the Courts of First Instance shall, insofar as
they may not be inconsistent with the provisions of Republic Act
No. 1125 and of these rules, be applicable
542

Rule 9, Section 1 of the Rules of Court provides:
“SECTION 1. Defenses and objections not pleaded.—Defenses

and objections not pleaded either in a motion to dismiss or in the
answer are deemed waived. However, when it appears from the
pleadings or the evidence on record that the court has no
jurisdiction over the subject matter, that there is another action
pending between the same parties for the same cause, or that the
action is barred by a prior judgment or by statute of limitations,
the court shall dismiss the claim.”
The CIR did not argue straight away in his Answer in

CTA Case No. 5762 that Toshiba had no right to the
credit/refund of its input VAT payments because the latter
was VAT-exempt and its export sales were VAT-exempt
transactions. The Pre-Trial Brief36 of the CIR was equally
bereft of such allegations or arguments. The CIR passed up
the opportunity to prove the supposed VAT-exemptions of
Toshiba and its export sales when the CIR chose not to
present any evidence at all during the trial before the
CTA.37 He missed another opportunity to present the said
issues before the CTA when he waived the submission of a
Memorandum.38 The CIR had waited until the CTA already
rendered its Decision dated October 16, 2000 in CTA Case
No. 5762, which granted the claim for credit/refund of
Toshiba, before asserting in his Motion for Reconsideration
that Toshiba was VAT-exempt and its export sales were
VAT-exempt transactions.
_______________
to cases pending before this Court, except that, in any case pending
before it, the Court may, in the exercise of its discretion, fix a
shorter period for the filing of pleadings and papers.
Under Batas Pambansa Blg. 129, otherwise known as The Judiciary
Reorganization Act of 1980, the Court of First Instance became the
Regional Trial Court.
37 Resolution dated May 10, 2000, signed by Presiding Judge Ernesto
D. Acosta and Associate Judges Amancio Q. Saga and Ramon O. de Veyra;
Id., at p. 72.
38 Rollo, p. 85.
543
VOL. 614, March 9, 2010 543

The CIR did not offer any explanation as to why he did

not argue the VAT-exemptions of Toshiba and its export
sales before and during the trial held by the CTA, only
doing so in his Motion for Reconsideration of the adverse
CTA judgment. Surely, said defenses or objections were
already available to the CIR when the CIR filed his Answer
to the Petition for Review of Toshiba in CTA Case No.

5762.
It is axiomatic in pleadings and practice that no new
issue in a case can be raised in a pleading which by due
diligence could have been raised in previous pleadings.39
The Court cannot simply grant the plea of the CIR that the
procedural rules be relaxed based on the general averment
of the interest of substantive justice. It should not be
forgotten that the first and fundamental concern of the
rules of procedure is to secure a just determination of every
action.40 Procedural rules are designed to facilitate the
adjudication of cases. Courts and litigants alike are
enjoined to abide strictly by the rules. While in certain
instances, the Court allows a relaxation in the application
of the rules, it never intends to forge a weapon for erring
litigants to violate the rules with impunity. The liberal
interpretation and application of rules apply only in proper
cases of demonstrable merit and under justifiable causes
and circumstances. While it is true that litigation is not a
game of technicalities, it is equally true that every case
must be prosecuted in accordance with the prescribed
procedure to ensure an orderly and speedy administration
of justice. Party litigants and their counsel are well advised
to abide by, rather than flaunt, procedural rules for these
rules illumine the path of the law and rationalize the
pursuit of justice.41
_______________
39 Director of Lands v. Court of Appeals, 363 Phil. 117, 128; 303 SCRA
495, 505 (1999).
40 Commissioner of Internal Revenue v. A. Soriano Corporation, 334
Phil. 965, 972; 267 SCRA 313, 319 (1997).
41 Land Bank of the Philippines v. Natividad, 497 Phil. 738, 744-745;
458 SCRA 441, 450 (2005).
544

The CIR judicially admitted that

Toshiba was VAT-registered and its
export sales were subject to VAT at
zero percent (0%) rate.
More importantly, the arguments of the CIR that
Toshiba was VAT-exempt and the latter’s export sales were
VAT-exempt transactions are inconsistent with the explicit

admissions of the CIR in the Joint Stipulation of Facts and
Issues (Joint Stipulation) that Toshiba was a registered
VAT entity and that it was subject to zero percent (0%)
VAT on its export sales.
The Joint Stipulation was executed and submitted by
Toshiba and the CIR upon being advised to do so by the
CTA at the end of the pre-trial conference held on June 23,
1999.42 The approval of the Joint Stipulation by the CTA,
in its Resolution43 dated July 12, 1999, marked the
culmination of the pre-trial process in CTA Case No.
5762.Pre-trial is an answer to the clarion call for the
speedy disposition of cases. Although it was discretionary
under the 1940 Rules of Court, it was made mandatory
under the 1964 Rules and the subsequent amendments in
1997. It has been hailed as “the most important procedural
innovation in Anglo-Saxon justice in the nineteenth
century.”44
The nature and purpose of a pre-trial have been laid
down in Rule 18, Section 2 of the Rules of Court:
“SECTION 2. Nature and purpose.—The pre-trial is

mandatory. The court shall consider:
(a) The possibility of an amicable settlement or of a
submission to alternative modes of dispute resolution;
_______________
42 Records, p. 33.
43 Signed by Presiding Judge Ernesto D. Acosta and Associate Judges Amancio
Q. Saga and Ramon O. De Veyra, Id., at p. 36.
44 Tiu v. Middleton, 369 Phil. 829, 835; 310 SCRA 580, 586 (1999).
545
VOL. 614, March 9, 2010 545

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(b) The simplification of the issues;

(c) The necessity or desirability of amendments to the
pleadings;
(d) The possibility of obtaining stipulations or
admissions of facts and of documents to avoid unnecessary
proof;
(e) The limitation of the number of witnesses;
(f) The advisability of a preliminary reference of issues to a
commissioner;
(g) The propriety of rendering judgment on the pleadings, or

summary judgment, or of dismissing the action should a valid
ground therefor be found to exist;
(h) The advisability or necessity of suspending the
proceedings; and
(i) Such other matters as may aid in the prompt disposition of
the action.” (Emphasis ours.)
The admission having been made in a stipulation of

facts at pre-trial by the parties, it must be treated as a
judicial admission.45 Under Section 4, Rule 129 of the Rules
of Court, a judicial admission requires no proof. The
admission may be contradicted only by a showing that it
was made through palpable mistake or that no such
admission was made. The Court cannot lightly set aside a
judicial admission especially when the opposing party
relied upon the same and accordingly dispensed with
further proof of the fact already admitted. An admission
made by a party in the course of the proceedings does not
require proof.46
In the instant case, among the facts expressly admitted
by the CIR and Toshiba in their CTA-approved Joint
Stipulation are that Toshiba “is a duly registered value-
added tax entity in accordance with Section 107 of the Tax
Code, as
_______________
45 SCC Chemicals Corporation v. Court of Appeals, 405 Phil. 514, 522-

523; 353 SCRA 70, 77 (2001).
46 Garcia v. Court of Appeals, 327 Phil. 1097, 1113; 258 SCRA 446, 459
(1996).
546

amended[,]”47 that “is subject to zero percent (0%) value-

added tax on its export sales in accordance with then
Section 100(a)(2)(A) of the Tax Code, as amended.”48 The
CIR was bound by these admissions, which he could not
eventually contradict in his Motion for Reconsideration of
the CTA Decision dated October 16, 2000, by arguing that
Toshiba was actually a VAT-exempt entity and its export
sales were VAT-exempt transactions. Obviously, Toshiba
could not have been subject to VAT and exempt from
VAT at the same time. Similarly, the export sales of

Toshiba could not have been subject to zero percent
(0%) VAT and exempt from VAT as well.
The CIR cannot escape the binding
effect of his judicial admissions.
The Court disagrees with the Court of Appeals when it
ruled in its Decision dated August 29, 2002 that the CIR
could not be bound by his admissions in the Joint
Stipulation because (1) the said admissions were “made
through palpable mistake”49 which, if countenanced,
“would result in falsehood, unfairness and injustice”;50 and
(2) the State could not be put in estoppel by the mistakes of
its officials or agents. This ruling of the Court of Appeals is
rooted in its conclusion that a “palpable mistake” had been
committed by the CIR in the signing of the Joint
Stipulation. However, this Court finds no evidence of the
commission of a mistake, much more, of a palpable one.
The CIR does not deny that his counsel, Atty. Joselito F.
Biazon, Revenue Attorney II of the BIR, signed the Joint
Stipulation, together with the counsel of Toshiba, Atty.
Patricia B. Bisda. Considering the presumption of
regularity
_______________
47 Records, p. 34.
48 Id.
49 Rollo, p. 49.
50 Id., at p. 51.
547
VOL. 614, March 9, 2010 547

in the performance of official duty,51 Atty. Biazon is

presumed to have read, studied, and understood the
contents of the Joint Stipulation before he signed the same.
It rests on the CIR to present evidence to the contrary.
Yet, the Court observes that the CIR himself never
alleged in his Motion for Reconsideration of the CTA
Decision dated October 16, 2000, nor in his Petition for
Review before the Court of Appeals, that Atty. Biazon
committed a mistake in signing the Joint Stipulation. Since
the CIR did not make such an allegation, neither did he
present any proof in support thereof. The CIR began to
aver the existence of a palpable mistake only after the
Court of Appeals made such a declaration in its Decision

dated August 29, 2002.
Despite the absence of allegation and evidence by the
CIR, the Court of Appeals, on its own, concluded that the
admissions of the CIR in the Joint Stipulation were due to
a palpable mistake based on the following deduction—
“Scrutinizing the Answer filed by [the CIR], we rule that the

Joint Stipulation of Facts and Issues signed by [the CIR] was
made through palpable mistake. Quoting paragraph 4 of its
Answer, [the CIR] states:
“4. He ADMITS the allegations contained in paragraph
5 of the petition only insofar as the cited provisions of Tax
Code is concerned, but SPECIFICALLY DENIES the rest of
the allegations therein for being mere opinions, arguments
or gratuitous assertions on the part of [Toshiba] and/or
because they are mere erroneous conclusions or
interpretations of the quoted law involved, the truth of the
matter being those stated hereunder
x x x x”
And paragraph 5 of the petition for review filed by [Toshiba]
before the CTA states:
_______________
51 Rule 131, Section 3(m) of the Rules of Court.
548

Internal Revenue
“5. Petitioner is subject to zero percent (0%) value-

added tax on its export sales in accordance with then
Section 100(a)(2)(A) of the Tax Code x x x.
x x x x”
As we see it, nothing in said Answer did [the CIR] admit that
the export sales of [Toshiba] were indeed zero-rated transactions.
At the least, what was admitted only by [the CIR] concerning
paragraph 4 of his Answer, is the fact that the provisions of the
Tax Code, as cited by [Toshiba] in its petition for review filed
before the CTA were correct.”52
The Court of Appeals provided no explanation as to why

the admissions of the CIR in his Answer in CTA Case No.
5762 deserved more weight and credence than those he
made in the Joint Stipulation. The appellate court failed to
appreciate that the CIR, through counsel, Atty. Biazon,
also signed the Joint Stipulation; and that absent evidence

to the contrary, Atty. Biazon is presumed to have signed
the Joint Stipulation willingly and knowingly, in the
regular performance of his official duties. Additionally, the
Joint Stipulation53 of Toshiba and the CIR was a more
recent pleading than the Answer54 of the CIR. It was
submitted by the parties after the pre-trial conference held
by the CTA, and subsequently approved by the tax court. If
there was any discrepancy between the admissions of the
CIR in his Answer and in the Joint Stipulation, the more
logical and reasonable explanation would be that the CIR
changed his mind or conceded some points to Toshiba
during the pre-trial conference which immediately
preceded the execution of the Joint Stipulation. To
automatically construe that the discrepancy was the result
of a palpable mistake is a wide leap which this Court is not
prepared to take without substantial basis.
_______________
52 Rollo, pp. 49-50.

53 Filed by the parties on July 7, 1999.
54 Filed by the CIR on May 11, 1999.
549
VOL. 614, March 9, 2010 549

The judicial admissions of the CIR in

the Joint Stipulation are not intrinsi-
cally false, wrong, or illegal, and are
consistent with the ruling on the VAT
treatment of PEZA-registered enter-
prises in the previous Toshiba case.
There is no basis for believing that to bind the CIR to his
judicial admissions in the Joint Stipulation—that Toshiba
was a VAT-registered entity and its export sales were zero-
rated VAT transactions—would result in “falsehood,
unfairness and injustice.” The judicial admissions of the
CIR are not intrinsically false, wrong, or illegal. On the
contrary, they are consistent with the ruling of this Court
in a previous case involving the same parties,
Commissioner of Internal Revenue v. Toshiba Information
Equipment (Phils.) Inc.55 (Toshiba case), explaining the
VAT treatment of PEZA-registered enterprises.
In the Toshiba case, Toshiba sought the refund of its

unutilized input VAT on its purchase of capital goods
and services for the first and second quarters of 1996,
based on Section 106(b) of the Tax Code of 1977, as
amended.56 In the Petition at bar, Toshiba is claiming
refund of its unutilized input VAT on its local purchase
of goods and services which are attributable to its
export sales for the first and second quarters of 1997,
pursuant to Section 106(a), in rela-
_______________
55 G.R. No. 150154, August 9, 2005, 466 SCRA 211, 230-231.

56 SEC. 106. Refunds or tax credits of creditable input tax.—
xxxx
(b) Capital goods.—A VAT-registered person may apply for the
issuance of a tax credit certificate or refund of input taxes paid on capital
goods imported or locally purchased, to the extent that such input taxes
have not been applied against output taxes. The application may be made
only within two (2) years after the close of the taxable quarter when the
importation or purchase was made.
550

tion to Section 100(a)(1)(A)(i) of the Tax Code of 1977, as

amended, which read—
“SEC. 106. Refunds or tax credits of creditable input tax.—(a)

Any VAT-registered person, whose sales are zero-rated or
effectively zero-rated, may, within two (2) years after the close of
the taxable quarter when the sales were made, apply for the
issuance of a tax credit certificate or refund of creditable input tax
due or paid attributable to such sales, except transitional input
tax, to the extent that such input tax has not been applied against
output tax: Provided, however, That in the case of zero-rated sales
under Section 100(a)(2)(A)(i),(ii) and (b) and Section 102(b)(1) and
(2), the acceptable foreign currency exchange proceeds thereof has
been duly accounted for in accordance with the regulations of the
Bangko Sentral ng Pilipinas (BSP): Provided, further, That where
the taxpayer is engaged in zero-rated or effectively zero-rated sale
and also in taxable or exempt sale of goods or properties of
services, and the amount of creditable input tax due or paid
cannot be directly and entirely attributed to any one of the
transactions, it shall be allocated proportionately on the basis of

the volume sales.
SEC. 100. Value-added tax on sale of goods or properties.—
(a) Rate and base of tax.—x x x
xxxx
(2) The following sales by VAT-registered persons shall be
subject to 0%:
Export sales.—The term “export sales” means:
(i) The sale and actual shipment of goods from the Philippines
to a foreign country, irrespective of any shipping arrangement
that may be agreed upon which may influence or determine the
transfer of ownership of the goods so exported and paid for in
acceptable foreign currency or its equivalent in goods or services,
and accounted for in accordance with the rules and regulations of
the Bangko Sentral ng Pilipnas (BSP).”
Despite the difference in the legal bases for the claims

for credit/refund in the Toshiba case and the case at bar,
the CIR raised the very same defense or objection in both—
that Toshiba and its transactions were VAT-exempt.
Hence, the rul-
551
VOL. 614, March 9, 2010 551

ing of the Court in the former case is relevant to the

present case.
At the outset, the Court establishes that there is a basic
distinction in the VAT-exemption of a person and the VAT-
exemption of a transaction—
“It would seem that petitioner CIR failed to differentiate

between VAT-exempt transactions from VAT-exempt entities. In
the case of Commissioner of Internal Revenue v. Seagate
Technology (Philippines), this Court already made such
distinction—
An exempt transaction, on the one hand, involves goods
or services which, by their nature, are specifically listed in
and expressly exempted from the VAT under the Tax Code,
without regard to the tax status—VAT-exempt or not—of
the party to the transaction…
An exempt party, on the other hand, is a person or entity
granted VAT exemption under the Tax Code, a special law
or an international agreement to which the Philippines is a
signatory, and by virtue of which its taxable transactions

become exempt from VAT x x x.”57
In effect, the CIR is opposing the claim for credit/refund

of input VAT of Toshiba on two grounds: (1) that Toshiba
was a VAT-exempt entity; and (2) that its export sales were
VAT-exempt transactions.
It is now a settled rule that based on the Cross Border
Doctrine, PEZA-registered enterprises, such as Toshiba,
are VAT-exempt and no VAT can be passed on to them. The
Court explained in the Toshiba case that—
PEZA-registered enterprise, which would necessarily be located

within ECOZONES, are VAT-exempt entities, not because of
Section 24 of Rep. Act No. 7916, as amended, which imposes the
five percent
_______________
57 Commissioner of Internal Revenue v. Toshiba Information Equipment (Phils.)

Inc., supra note 55 at 222-223, citing Commissioner of Internal Revenue v. Seagate
Technology (Philippines), 491 Phil. 317, 335; 451 SCRA 132, 145 (2005).
552

Internal Revenue
(5%) preferential tax rate on gross income of PEZA-registered

enterprises, in lieu of all taxes; but, rather, because of Section 8 of
the same statute which establishes the fiction that ECOZONES
are foreign territory.
xxxx
The Philippine VAT system adheres to the Cross Border
Doctrine, according to which, no VAT shall be imposed to form
part of the cost of goods destined for consumption outside of the
territorial border of the taxing authority. Hence, actual export of
goods and services from the Philippines to a foreign country must
be free of VAT; while, those destined for use or consumption
within the Philippines shall be imposed with ten percent (10%)
VAT.
Applying said doctrine to the sale of goods, properties, and
services to and from the ECOZONES, the BIR issued Revenue
Memorandum Circular (RMC) No. 74-99, on 15 October 1999. Of
particular interest to the present Petition is Section 3 thereof,
which reads—
SECTION 3. Tax Treatment of Sales Made by a
VAT Registered Supplier from the Customs Territory,
to a PEZA Registered Enterprise.—

(1) If the Buyer is a PEZA registered enterprise which
is subject to the 5% special tax regime, in lieu of all taxes,
except real property tax, pursuant to R.A. No. 7916, as
amended:
(a) Sale of goods (i.e., merchandise).—This shall
be treated as indirect export hence, considered subject to
zero percent (0%) VAT, pursuant to Sec. 106(A)(2)(a)(5),
NIRC and Sec. 23 of R.A. No. 7916, in relation to ART. 77(2)
of the Omnibus Investments Code.
(b) Sale of service.—This shall be treated subject to
zero percent (0%) VAT under the “cross border doctrine” of
the VAT System, pursuant to VAT Ruling No. 032-98 dated
Nov. 5, 1998.
(2) If Buyer is a PEZA registered enterprise which is
not embraced by the 5% special tax regime, hence, subject
to taxes under the NIRC, e.g., Service Establishments
which are subject to taxes under the NIRC rather than the
5% special tax regime:
(a) Sale of goods (i.e., merchandise).—This shall be
treated as indirect export hence, considered subject to zero
per-
553
VOL. 614, March 9, 2010 553

Internal Revenue
cent (0%) VAT, pursuant to Sec. 106(A)(2)(a)(5), NIRC and

Sec. 23 of R.A. No. 7916 in relation to ART. 77(2) of the
Omnibus Investments Code.
(b) Sale of Service.—This shall be treated subject to
zero percent (0%) VAT under the “cross border doctrine” of
the VAT System, pursuant to VAT Ruling No. 032-98 dated
Nov. 5, 1998.
(3) In the final analysis, any sale of goods, property or
services made by a VAT registered supplier from the
Customs Territory to any registered enterprise operating in
the ecozone, regardless of the class or type of the latter’s
PEZA registration, is actually qualified and thus legally
entitled to the zero percent (0%) VAT. Accordingly, all sales
of goods or property to such enterprise made by a VAT
registered supplier from the Customs Territory shall be
treated subject to 0% VAT, pursuant to Sec. 106(A)(2)(a)(5),
NIRC, in relation to ART. 77(2) of the Omnibus
Investments Code, while all sales of services to the said
enterprises, made by VAT registered suppliers from the
Customs Territory, shall be treated effectively subject to the
0% VAT, pursuant to Section 108(B)(3), NIRC, in relation to

the provisions of R.A. No. 7916 and the “Cross Border
Doctrine” of the VAT system.
This Circular shall serve as a sufficient basis to entitle
such supplier of goods, property or services to the benefit of
the zero percent (0%) VAT for sales made to the
aforementioned ECOZONE enterprises and shall serve as
sufficient compliance to the requirement for prior approval
of zero-rating imposed by Revenue Regulations No. 7-95
effective as of the date of the issuance of this Circular.
Indubitably, no output VAT may be passed on to an ECOZONE
enterprise since it is a VAT-exempt entity. x x x.”58
The Court, nevertheless, noted in the Toshiba case that

the rule which considers any sale by a supplier from the
Customs Territory to a PEZA-registered enterprise as
export sale, which should not be burdened by output VAT,
was only
_______________
58 Commissioner of Internal Revenue v. Toshiba Information

Equipment (Phils.) Inc., Id., at pp. 223-226.
554

clearly established on October 15, 1999, upon the

issuance by the BIR of RMC No. 74-99. Prior to October
15, 1999, whether a PEZA-registered enterprise was
exempt or subject to VAT depended on the type of fiscal
incentives availed of by the said enterprise.59 The old rule,
then followed by the BIR, and recognized and affirmed by
the CTA, the Court of Appeals, and this Court, was
described as follows—
“According to the old rule, Section 23 of Rep. Act No. 7916, as

amended, gives the PEZA-registered enterprise the option to
choose between two sets of fiscal incentives: (a) The five percent
(5%) preferential tax rate on its gross income under Rep. Act No.
7916, as amended; and (b) the income tax holiday provided under
Executive Order No. 226, otherwise known as the Omnibus
Investment Code of 1987, as amended.
The five percent (5%) preferential tax rate on gross income
under Rep. Act No. 7916, as amended, is in lieu of all taxes.
Except for real property taxes, no other national or local tax may
be imposed on a PEZA-registered enterprise availing of this
particular fiscal incentive, not even an indirect tax like VAT.
Alternatively, Book VI of Exec. Order No. 226, as amended,
grants income tax holiday to registered pioneer and non-pioneer
enterprises for six-year and four-year periods, respectively. Those
availing of this incentive are exempt only from income tax, but
shall be subject to all other taxes, including the ten percent (10%)
VAT.
This old rule clearly did not take into consideration the Cross
Border Doctrine essential to the VAT system or the fiction of the
ECOZONE as a foreign territory. It relied totally on the choice of
fiscal incentives of the PEZA-registered enterprise. Again, for
emphasis, the old VAT rule for PEZA-registered enterprises was
based on their choice of fiscal incentives: (1) If the PEZA-
registered enterprise chose the five percent (5%) preferential tax
on its gross income, in lieu of all taxes, as provided by Rep. Act
No. 7916, as amended, then it would be VAT-exempt; (2) If the
PEZA-registered enterprise availed of the income tax holiday
under Exec. Order No. 226, as amended, it shall be subject to VAT
at ten percent (10%). Such distinction was abolished by RMC No.
74-99, which categorically de-
_______________
59 Id., at pp. 229-230.
555
VOL. 614, March 9, 2010 555

Internal Revenue
clared that all sales of goods, properties, and services made by a

VAT-registered supplier from the Customs Territory to an
ECOZONE enterprise shall be subject to VAT, at zero percent
(0%) rate, regardless of the latter’s type or class of PEZA
registration; and, thus, affirming the nature of a PEZA-registered
or an ECOZONE enterprise as a VAT-exempt entity.”60
To recall, Toshiba is herein claiming the refund of

unutilized input VAT payments on its local purchases of
goods and services attributable to its export sales for the
first and second quarters of 1997. Such export sales
took place before October 15, 1999, when the old rule on
the VAT treatment of PEZA-registered enterprises still
applied. Under this old rule, it was not only possible, but
even acceptable, for Toshiba, availing itself of the income
tax holiday option under Section 23 of Republic Act No.
7916, in relation to Section 39 of the Omnibus Investments

Code of 1987, to be subject to VAT, both indirectly (as
purchaser to whom the seller shifts the VAT burden) and
directly (as seller whose sales were subject to VAT, either
at ten percent [10%] or zero percent [0%]).
A VAT-registered seller of goods and/or services who
made zero-rated sales can claim tax credit or refund of the
input VAT paid on its purchases of goods, properties, or
services relative to such zero-rated sales, in accordance
with Section 4.102-2 of Revenue Regulations No. 7-95,
which provides—
“Sec. 4.102-2. Zero-rating.—(a) In general.—A zero-rated sale

by a VAT-registered person, which is a taxable transaction for
VAT purposes, shall not result in any output tax. However, the
input tax on his purchases of goods, properties or services related
to such zero-rated sale shall be available as tax credit or refund in
accordance with these regulations.”
The BIR, as late as July 15, 2003, when it issued RMC

No. 42-2003, accepted applications for credit/refund of
input VAT on purchases prior to RMC No. 74-99, filed by
PEZA-
_______________
60 Id., at pp. 230-231.
556

registered enterprises which availed themselves of the

income tax holiday. The BIR answered Question Q-5(1) of
RMC No. 42-2003 in this wise—
Q-5: Under Revenue Memorandum Circular (RMC) No. 74-99,

purchases by PEZA-registered firms automatically qualify
as zero-rated without seeking prior approval from the BIR
effective October 1999.
1) Will the OSS-DOF Center still accept applications from
PEZA-registered claimants who were allegedly billed
VAT by their suppliers before and during the effectivity of
the RMC by issuing VAT invoices/receipts?
xxxx
A-5(1): If the PEZA-registered enterprise is paying the 5%
preferential tax in lieu of all other taxes, the said PEZA-
registered taxpayer cannot claim TCC or refund for the

VAT paid on purchases. However, if the taxpayer is
availing of the income tax holiday, it can claim VAT
credit provided:
a. The taxpayer-claimant is VAT-registered;
b. Purchases are evidenced by VAT invoices or
receipts, whichever is applicable, with shifted VAT
to the purchaser prior to the implementation of
RMC No. 74-99; and
c. The supplier issues a sworn statement under
penalties of perjury that it shifted the VAT and
declared the sales to the PEZA-registered purchaser
as taxable sales in its VAT returns.
For invoices/receipts issued upon the effectivity of RMC No. 74-99, the
claims for input VAT by PEZA-registered companies, regardless of the
type or class of PEZA-registration, should be denied.” (Emphases ours.)
Consequently, the CIR cannot herein insist that all

PEZA-registered enterprises are VAT-exempt in every
instance. RMC No. 42-2003 contains an express
acknowledgement by the BIR that prior to RMC No. 74-99,
there were PEZA-
557
VOL. 614, March 9, 2010 557

registered enterprises liable for VAT and entitled to

credit/refund of input VAT paid under certain conditions.
This Court already rejected in the Toshiba case the
argument that sale transactions of a PEZA-registered
enterprise were VAT-exempt under Section 103(q) of the
Tax Code of 1977, as amended, ratiocinating that—
“Section 103(q) of the Tax Code of 1977, as amended, relied

upon by petitioner CIR, relates to VAT-exempt transactions.
These are transactions exempted from VAT by special laws or
international agreements to which the Philippines is a signatory.
Since such transactions are not subject to VAT, the sellers cannot
pass on any output VAT to the purchasers of goods, properties, or
services, and they may not claim tax credit/refund of the input
VAT they had paid thereon.
Section 103(q) of the Tax Code of 1977, as amended, cannot
apply to transactions of respondent Toshiba because although the
said section recognizes that transactions covered by special laws
may be exempt from VAT, the very same section provides that
those falling under Presidential Decree No. 66 are not.

Presidential Decree No. 66, creating the Export Processing
Zone Authority (EPZA), is the precursor of Rep. Act No.
7916, as amended, under which the EPZA evolved into the
PEZA. Consequently, the exception of Presidential Decree
No. 66 from Section 103(q) of the Tax Code of 1977, as
amended, extends likewise to Rep. Act No. 7916, as
amended.”61 (Emphasis ours.)
In light of the judicial admissions of

Toshiba, the CTA correctly confined
itself to the other factual issues submit-
ted for resolution by the parties.
In accord with the admitted facts—that Toshiba was a
VAT-registered entity and that its export sales were zero-
rated transactions—the stated issues in the Joint
Stipulation were limited to other factual matters,
particularly, on the
_______________
61 Id., at p. 223.
558

compliance by Toshiba with the rest of the requirements

for credit/refund of input VAT on zero-rated transactions.
Thus, during trial, Toshiba concentrated on presenting
evidence to establish that it incurred P3,875,139.65 of
input VAT for the first and second quarters of 1997 which
were directly attributable to its export sales; that said
amount of input VAT were not carried over to the
succeeding quarters; that said amount of input VAT has
not been applied or offset against any output VAT liability;
and that said amount of input VAT was properly
substantiated by official receipts and invoices.
After what truly appears to be an exhaustive review of
the evidence presented by Toshiba, the CTA made the
following findings—
(1) The amended quarterly VAT returns of Toshiba for
1997 showed that it made no other sales, except zero-rated
export sales, for the entire year, in the sum of
P2,083,305,000.00 for the first quarter and
P5,411,372,000.00 for the second quarter. That being the
case, all input VAT allegedly incurred by Toshiba for the

first two quarters of 1997, in the amount of P3,875,139.65,
was directly attributable to its zero-rated sales for the
same period.
(2) Toshiba did carry-over the P3,875,139.65 input
VAT it reportedly incurred during the first two quarters of
1997 to succeeding quarters, until the first quarter of 1999.
Despite the carry-over of the subject input VAT of
P3,875,139.65, the claim of Toshiba was not affected
because it later on deducted the said amount as “VAT
Refund/TCC Claimed” from its total available input VAT of
P6,841,468.17 for the first quarter of 1999.
(3) Still, the CTA could not allow the credit/refund of
the total input VAT of P3,875,139.65 being claimed by
Toshiba because not all of said amount was actually
incurred by the company and duly substantiated by
invoices and official receipts. From the P3,875,139.65
claim, the CTA deducted the amounts of (a) P189,692.92,
which was in excess of the P3,685,446.23 input VAT
Toshiba originally claimed in its
559
VOL. 614, March 9, 2010 559

application for credit/refund filed with the DOF One-Stop

Shop; (b) P396,882.58, which SGV & Co., the
commissioned CPA, disallowed for being improperly
substantiated, i.e., supported only by provisional
acknowledgement receipts, or by documents other than
official receipts, or not supported by TIN or TIN VAT or by
any document at all; (c) P1,887,545.65, which the CTA
itself verified as not being substantiated in accordance with
Section 4.104-562 of Revenue Regulations No. 7-95, in
relation to Sections 10863 and 23864 of the Tax Code of
_______________
62 SECTION 4.104-5. Substantiation of claims for input tax credit.—

(a) Input taxes shall be allowed only if the domestic purchase of goods,
properties or services is made in the course of trade or business. The input
tax should be supported by an invoice or receipt showing the information
as required under Sections 108(a) and 237 of the Code. Input tax on
purchases of real property should be supported by a copy of the public
instrument, i.e., deed of absolute sale, deed of conditional sale,
contract/agreement to sell, etc., together with the VAT receipt issued by

the seller.
A cash register machine tape issued to a VAT-registered buyer by a
VAT-registered seller from a machine duly registered with the BIR in lieu
of the regular sales invoice, shall constitute valid proof of substantiation of
tax credit only if the name and TIN of the purchaser is indicated in the
receipt and authenticated by a duly authorized representative of the
seller.
(b) Input tax on importations shall be supported with the import
entry or other equivalent document showing actual payment of VAT on
the imported goods.
(c) Presumptive input tax shall be supported by an inventory of goods
as shown in a detailed list to be submitted to the BIR.
(d) Input tax on “deemed sale” transactions shall be substantiated
with the required invoices.
(e) Input tax from payments made to non-residents shall be supported
by a copy of the VAT declaration/return filed by the resident
licensee/lessee in behalf of the non-resident licensor/lessor evidencing
remittance of the VAT due.
63 SEC. 108. Invoicing and accounting requirements for VAT-
registered persons.—(a) Invoicing requirements.—A VAT-registered person
shall, for every sale, issue an invoice or receipt. In addition to
600

_______________
the information required under Section 238, the following information

shall be indicated in the invoice or receipt:
(1) A statement that the seller is a VAT-registered person, followed by
his taxpayer’s identification number (TIN); and
(2) The total amount which the purchaser pays or is obligated to pay
to the seller with the indication that such amount includes the value-
added tax.
(b) Accounting requirements.—Notwithstanding the provision of
Section 223, all persons subject to the value-added tax under Sections 100
and 102 shall, in addition to the regular accounting records required,
maintain a subsidiary sales journal and subsidiary purchase journal on
which the daily sales and purchases are recorded. The subsidiary journals
shall contain such information as may be required by the Secretary of
Finance.
64 SEC. 238. Issuance of receipts or sales or commercial invoices.—All
persons subject to an internal revenue tax shall, for each sale or transfer
of merchandise or for services rendered valued at P25.00 or more, issue
duly registered receipts or sales or commercial invoices, prepared at least

in duplicate, showing the date of transaction, quantity, unit cost and
description of merchandise or nature of service: Provided, however, That
in the case of sales, receipts or transfers in the amount of P100.00 or
more, or, regardless of amount, where the sale or transfer is made by a
person liable to value-added tax to another person also liable to value-
added tax; or where the receipt is issued to cover payment made as
rentals, commissions, compensations or fees, receipts or invoices shall be
issued which shall show the name, business style, if any, and address of
the purchaser, customer, or client: Provided, further, That where the
purchaser is a VAT-registered person, in addition to the information
herein required the invoice or receipt shall further show the taxpayer’s
identification number of the purchaser.
The original of each receipt or invoice shall be issued to the purchaser,
customer or client at the time the transaction is effected, who, if engaged
in business or in the exercise of profession, shall keep and preserve the
same in his place of business for a period of 3 years from the close of the
taxable year in which such invoice or receipt was issued while the
duplicate shall be kept and preserved by the issuer, also in his place of
business for a like period.
The Commissioner may, in meritorious cases exempt any person
subject to an internal revenue tax from compliance with the provisions of
this section.
561
VOL. 614, March 9, 2010 561

1977, as amended; and (d) P15,736.42, which Toshiba

already applied to its output VAT liability for the fourth
quarter of 1998.
(4) Ultimately, Toshiba was entitled to the
credit/refund of unutilized input VAT payments
attributable to its zero-rated sales in the amounts of
P1,158,016.82 and P227,265.26, for the first and second
quarters of 1997, respectively, or in the total amount of
P1,385,282.08.
Since the aforementioned findings of fact of the CTA are
borne by substantial evidence on record, unrefuted by the
CIR, and untouched by the Court of Appeals, they are given
utmost respect by this Court.
The Court will not lightly set aside the conclusions
reached by the CTA which, by the very nature of its
functions, is dedicated exclusively to the resolution of tax
problems and has accordingly developed an expertise on
the subject unless there has been an abuse or improvident
exercise of authority.65 In Barcelon, Roxas Securities, Inc.

(now known as UBP Securities, Inc.) v. Commissioner of
Internal Revenue,66 this Court more explicitly pronounced
—
“Jurisprudence has consistently shown that this Court accords

the findings of fact by the CTA with the highest respect. In Sea-
Land Service Inc. v. Court of Appeals [G.R. No. 122605, 30 April
2001, 357 SCRA 441, 445-446], this Court recognizes that the
Court of Tax Appeals, which by the very nature of its function is
dedicated exclusively to the consideration of tax problems, has
necessarily developed an expertise on the subject, and its
conclusions will not be overturned unless there has been an abuse
or improvident exercise of authority. Such findings can only be
disturbed on appeal if they are
_______________
65 Commissioner of Internal Revenue v. Cebu Toyo Corporation, 491 Phil. 625,

640; 451 SCRA 447, 463 (2005).
66 G.R. No. 150764, August 7, 2006, 498 SCRA 126, 135-136.
562

Internal Revenue
not supported by substantial evidence or there is a showing of

gross error or abuse on the part of the Tax Court. In the absence
of any clear and convincing proof to the contrary, this Court must
presume that the CTA rendered a decision which is valid in every
respect.”
WHEREFORE, the assailed Decision dated August 29,

2002 and the Resolution dated February 19, 2003 of the
Court of Appeals in CA-G.R. SP No. 63047 are REVERSED
and SET ASIDE, and the Decision dated October 16, 2000
of the Court of Tax Appeals in CTA Case No. 5762 is
REINSTATED. Respondent Commissioner of Internal
Revenue is ORDERED to REFUND or, in the alternative,
to ISSUE a TAX CREDIT CERTIFICATE in favor of
petitioner Toshiba Information Equipment (Phils.), Inc. in
the amount of P1,385,282.08, representing the latter’s
unutilized input VAT payments for the first and second
quarters of 1997. No pronouncement as to costs.
SO ORDERED.
Puno (C.J., Chairperson), Carpio-Morales, Bersamin

and Villarama, Jr., JJ., concur.
Judgment and resolution reversed and set aside, that of

CTA reinstated.
Note.—Pre-trial is not a mere technicality in court

proceeding for it is essential in the simplification and the
speedy disposition of disputes. (RN Development
Corporation vs. A.I.I. System, Inc., 555 SCRA 513 [2008])
——o0o——
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2/6/2019 SUPREME COURT REPORTS ANNOTATED VOLUME 614

Puno (C.J., Chairperson), Carpio-Morales, Leonardo-

Petition denied, judgment affirmed.

Note.—Prescription does not run against the

G.R. No. 157594. March 9, 2010.*

TOSHIBA INFORMATION EQUIPMENT (PHILS.), INC.,

Remedial Law; Pleadings and Practice; It is axiomatic in

VOL. 614, March 9, 2010 527

Toshiba Information Equipment (Phils.), Inc. vs. Commissioner of

in pleadings and practice that no new issue in a case can be raised

PETITION for review on certiorari of a decision of the

528 SUPREME COURT REPORTS ANNOTATED

Agan & Montenegro Law Offices for petitioner.

LEONARDO-DE CASTRO, J.:

1 Rollo, pp. 11-32.

VOL. 614, March 9, 2010 529

HDD-CD-ROM and personal computer printed circuit

530 SUPREME COURT REPORTS ANNOTATED

The next day, on March 31, 1999, Toshiba likewise filed

“[A]fter due hearing, judgment be rendered ordering [herein

14 Records, pp. 1-5.

VOL. 614, March 9, 2010 531

chase of taxable goods and services for the period January 1 to

The Commissioner of Internal Revenue (CIR) opposed

5. [Toshiba’s] alleged claim for refund/tax credit is subject to

Upon being advised by the CTA,20 Toshiba and the CIR

1. [Toshiba] is a duly registered value-added tax entity in

532 SUPREME COURT REPORTS ANNOTATED

2. [Toshiba] is subject to zero percent (0%) value-added tax on

7. [Toshiba] is subject to zero percent (0%) value-added tax

In the same pleading, Toshiba and the CIR jointly

Whether or not [Toshiba] has incurred input taxes in the amount

During the trial before the CTA, Toshiba presented

VOL. 614, March 9, 2010 533

Toshiba were subject to zero percent (0%) VAT based on

CTA, though, reduced the amount to be credited or

“WHEREFORE, [Toshiba’s] claim for refund of unutilized

1st Quarter 2nd Total

Respondent Commissioner of Internal Revenue is ORDERED

24 Id., at pp. 91-92.

534 SUPREME COURT REPORTS ANNOTATED

Both Toshiba and the CIR sought reconsideration of the

Section 24 of Republic Act No. 791627

25 Id., at pp. 99-100.

VOL. 614, March 9, 2010 535

Section 4.103-1 of Revenue Regulations No. 7-95

The CIR contended that under Section 24 of Republic

28 Signed by Presiding Judge Ernesto D. Acosta and Associate Judges

536 SUPREME COURT REPORTS ANNOTATED

Commissioner of Internal Revenue

“SECTION 23. Fiscal Incentives.—Business establishments

Among the fiscal incentives granted to PEZA-registered

“Art. 39. Incentives to Registered Enterprises.—All registered

VOL. 614, March 9, 2010 537

Board, the income tax exemption will be extended for another

(i) The project meets the prescribed ratio of capital equipment

The CTA pointed out that Toshiba availed itself of the

29 Rollo, pp. 107-118.

538 SUPREME COURT REPORTS ANNOTATED