SMI-ED Technology v.

CIR
G.R. No. 175410
November 12, 2014

Doctrines:

In an action for the refund of taxes allegedly erroneously paid, the Court of
Tax Appeals may determine whether there are taxes that should have been
paid in lieu of the taxes paid. Determining the proper category of tax that
should have been paid is not an assessment. It is incidental to determining
whether there should be a refund.
A Philippine Economic Zone Authority (PEZA)-registered corporation that has
never commenced operations may not avail the tax incentives and
preferential rates given to PEZA-registered enterprises. Such corporation is
subject to ordinary tax rates under the National Internal Revenue Code of
1997.

Facts:

SMI-Ed Philippines is a PEZA-registered corporation authorized "to engage in

the business of manufacturing ultra high-density microprocessor unit
package."
After its registration on June 29, 1998, SMI-Ed Philippines constructed
buildings and purchased machineries and equipment.
SMI-Ed Philippines "failed to commence operations." Its factory was
temporarily closed, effective October 15, 1999. On August 1, 2000, it sold its
buildings and some of its installed machineries and equipment to Ibiden
Philippines, Inc., another PEZA-registered enterprise. SMI-Ed Philippines was
dissolved on November 30, 2000.
In its quarterly income tax return for year 2000, SMI-Ed Philippines subjected
the entire gross sales of itsproperties to 5% final tax on PEZA registered
corporations. SMI-Ed Philippines paid taxes amounting to P44,677,500.00.
On February 2, 2001, after requesting the cancellation of its PEZA registration
and amending its articles of incorporation to shorten its corporate term, SMI-
Ed Philippines filed an administrative claim for the refund of P44,677,500.00
with the Bureauof Internal Revenue (BIR). SMIEd Philippines alleged that the
amountwas erroneously paid.
The BIR did not act on SMI-Ed Philippines claim, which prompted the latter to
file a petition for review before the Court of Tax Appeal.
CTA denied SMI-ED claim for refund. It held that:
1. fiscal incentives given to PEZA-registered enterprises may be availed only
by PEZA-registered enterprises that had already commenced
operations.16 Since SMI-Ed Philippines had not commenced operations, it
was not entitled to the incentives of either the income tax holiday or the
 5% preferential tax rate. 17 Payment of the 5% preferential tax amounting
to P44,677,500.00 was erroneous.
2. It found that the properties sold by SMI-ED were capital assets under
Section 39(A)(1) of the National Internal Revenue Code of 1997, hence it
subjected the sale of SMIEd Philippines assets to 6% capital gains tax. It
was found liable for capital gains tax amounting to P53,613,000.00.20.
Therefore, SMIEd Philippines must still pay the balance of P8,935,500.00
as deficiency tax.
SMI-ED filed a peitition for review with the CTA en banc.
CTA en banc affirmed the CTA second division.
SMI-Ed Philippines filed a petition for review before the Supreme Court
praying for the grant of its claim for refund and the reversal of the Court of
Tax Appeals En Bancs decision.

SMI-EDs Arguments:

It argued that the Court of Tax Appeals Second Division erroneously assessed
the 6% capital gains tax on the sale of SMI-Ed Philippines equipment,
machineries, and buildings. It also argued that the Court of Tax Appeals
Second Division cannot make an assessment at the first instance. Even if the
Court of Tax Appeals Second Division has such power, the period to make an
assessment had already prescribed.

Issues w/ Ruling:

1. WON CTA En Banc grievously erred and acted beyond its jurisdiction
when it assessed for deficiency tax in the first instance- NO

The term "assessment" refers to the determination of amounts due from a person
obligated to make payments. In the context of national internal revenue collection,
it refers the determination of the taxes due from a taxpayer under the National
Internal Revenue Code of 1997. The power and duty to assess national internal
revenue taxes are lodged with the BIR.

The Court of Tax Appeals has no powerto make an assessment at the first instance.
On matters such as tax collection, tax refund, and others related to the national
internal revenue taxes, the Court of Tax Appeals jurisdiction is appellate in nature.

Based on the law, the following must be present for the Court of Tax Appeals to
have jurisdiction over a case involving the BIRs decisions or inactions:

a) A case involving any of the following:

 i. Disputed assessments;

ii. Refunds of internal revenue taxes, fees, or other charges, penalties

in relation thereto; and

iii. Other matters arising under the National Internal Revenue Code of
1997.

b) Commissioner of Internal Revenues decision or inaction in a case

submitted to him or her

Thus, the BIR first has to make an assessment of the taxpayers liabilities.
When the BIR makes the assessment, the taxpayer is allowed to dispute that
assessment before the BIR. If the BIR issues a decision that is unfavorable to the
taxpayer or if the BIR fails to act on a dispute brought by the taxpayer, the BIRs
decision or inaction may be brought on appeal to the Court of Tax Appeals. The
Court of Tax Appeals then acquires jurisdiction over the case.

When the BIRs unfavorable decision is brought on appeal to the Court of Tax
Appeals, the Court of Tax Appeals reviews the correctness of the BIRs assessment
and decision. In reviewing the BIRs assessment and decision, the Court of Tax
Appeals had to make its own determination of the taxpayers tax liabilities. The
Court of Tax Appeals may not make such determination before the BIR makes its
assessment and before a dispute involving such assessment is brought to the Court
of Tax Appeals on appeal.

In this case, the Court of Tax Appeals jurisdiction was acquired because
petitioner brought the case on appeal before the Court of Tax Appeals after the BIR
had failed to act on petitioners claim for refund of erroneously paid taxes. The
Court of Tax Appeals did not acquire jurisdiction as a result of a disputed
assessment of a BIR decision.

As earlier established, the Court of Tax Appeals has no assessment powers. In

stating that petitioners transactions are subject to capital gains tax, however, the
Court of Tax Appeals was not making an assessment. It was merely determining the
proper category of tax that petitioner should have paid, in view of its claim that it
erroneously imposed upon itself and paid the 5% final tax imposed upon PEZA-
registered enterprises.

The determination of the proper category of tax that petitioner should have paid
is an incidental matter necessary for the resolution of the principal issue, which is
whether petitioner was entitled to a refund.

The issue of petitioners claim for tax refund is intertwined with the issue of the
proper taxes that are due from petitioner. A claim for tax refund carries the
assumption that the tax returns filed were correct.55 If the tax return filed was not
proper, the correctness of the amount paid and, therefore, the claim for refund
become questionable. In that case, the court must determine if a taxpayer claiming
refund of erroneously paid taxes is more properly liable for taxes other than that
paid.

In this case, petitioners claim that it erroneously paid the 5% final tax is an
admission that the quarterly tax return it filed in 2000 was improper. Hence, to
determine if petitioner was entitled to the refund being claimed, the Court of Tax
Appeals has the duty to determine if petitioner was indeed not liable for the 5% final
tax and, instead, liable for taxes other than the 5% final tax. As in South African
Airways, petitioners request for refund can neither be granted nor denied outright
without such determination.58

Any liability in excess of the refundable amount, however, may not be collected
in a case involving solely the issue of the taxpayers entitlement to refund. The
question of tax deficiencyis distinct and unrelated to the question of petitioners
entitlement to refund. Tax deficiencies should be subject to assessment procedures
and the rules of prescription. The court cannot be expected to perform the BIRs
duties whenever it fails to do so either through neglect or oversight. Neither can
court processes be used as a tool to circumvent laws protecting the rights of
taxpayers.

2. WON SMI-ED is entitled to the benefits given to PEZA-registered

enterprises including the 5% preferential tax rate.

NO. This is because it never began its operation.

Essentially, the purpose of Republic Act No. 7916 is to promote development

and encourage investments and business activities that will generate
employment.59 Giving fiscal incentives to businesses is one of the means devised
to achieve this purpose. It comes with the expectation that persons who will avail
these incentives will contribute to the purposes achievement. Hence, to avail the
fiscal incentives under Republic Act No. 7916, the law did not say that mere PEZA
registration is sufficient.

The fiscal incentives and the 5% preferential tax rate are available only to
businesses operating within the Ecozone. A business is considered in operation
when it starts entering into commercial transactions that are not merely incidental
to but are related to the purposes of the business. It is similar to the definition of
"doing business," as applied in actions involvingthe right of foreign corporations to
maintain court actions. The terms "doing" or "engaging in" or "transacting"
business": impl[y] a continuity of commercial dealings and arrangements, and
contemplates, to that extent, the performance of acts or works or the exercise of
some of the functions normally incident to, and in progressive prosecution of, the
purpose and object of its organization. Petitioner never started its operations since
its registration on June 29, 199863 because of the Asian financial crisis . It is not
entitled to the preferential tax rate of 5% on gross income in lieu of all taxes.
Because petitioner is not entitled to a preferential rate, it is subject to ordinary tax
rates under the National Internal Revenue Code of 1997.

3. WON CTA erred in imposing the capital gains tax on the sale of SMI-
Eds buildings, equipments, and machineries-
Withe respect to the sale of buildings and and land, wala nasayup ang CA
With respect to the sale of machineries and equipments, nasayup ang CA

For petitioners properties to be subjected to capital gains tax, the properties

must form part of petitioners capital assets. The properties involved in this case
include petitioners buildings, equipment, and machineries. They are not among the
exclusions enumerated in Section 39(A)(1) of the National Internal Revenue Code of
1997. None of the properties were used in petitioners trade or ordinary course of
business because petitioner never commenced operations. They were not part of
the inventory. None of themwere stocks in trade. Based on the definition of capital
assets under Section 39 of the National Internal Revenue Code of 1997, they are
capital assets.

As regards machineries and equipments, these should not be subjected to the

capital gains tax since these are not real properties. Only the presumed gain from
the sale of petitioners land and/or building may be subjected to the 6% capital
gains tax. The income from the sale of petitioners machineries and equipment is
subject to the provisions on normal corporate income tax.

To determine, therefore, if petitioner is entitled to refund, the amount of capital

gains tax for the sold land and/or building of petitioner and the amount of corporate
income tax for the sale of petitioners machineries and equipment should be
deducted from the total final tax paid.

Petitioner indicated, however, in its March 1, 2001 income tax return for the
11-month period ending on November 30, 2000 that it suffered a net loss of
P2,233,464,538.00.69 This declaration was made under the pain of perjury. The BIR
did not make a deficiency assessment for this declaration. Neither did the BIR
dispute this statement in its pleadings filed before this court. There is, therefore, no
reason todoubt the truth that petitioner indeed suffered a net loss in 2000. Since
petitioner had not started its operations, it was also not subject to the minimum
corporate income tax of 2% on gross income.70 Therefore, petitioner is not liable for
any income tax.
 4. WON the government can still collect for the deficiency taxes (kay
5% preferential tax rate raman tu ya gibayran when it should have
been 6% capital gains tax rate)- NOT ANYMORE

Section 203 of the National Internal Revenue Code of 1997 provides that as a
general rule, the BIR has three (3) years from the last day prescribed by law for the
filing of a return to make an assessment. If the return is filed beyond the last day
prescribed by law for filing, the three-year period shall run from the actual date of
filing.

This court said that the prescriptive period to make an assessment of internal
revenue taxes is provided "primarily to safeguard the interests of taxpayers from
unreasonable investigation."71 This court explained in Commissioner of Internal
Revenue v. FMF Development Corporation72 the reason behind the provisions on
prescriptive periods for tax assessments: Accordingly, the government must assess
internal revenue taxes on time so as not to extend indefinitely the period of
assessment and deprive the taxpayer of the assurance that it will no longer be
subjected to further investigation for taxes after the expiration of reasonable period
of time.

Thus, the law on prescription, being a remedial measure, should be liberally

construed in order to afford such protection. As a corollary, the exceptions to the
law on prescription should perforce be strictly construed.

The BIR had three years from the filing of petitioners final tax return in 2000 to
assess petitioners taxes. Nothing stopped the BIR from making the correct
assessment. The elevation of the refund claim with the Court of Tax Appeals was not
a bar against the BIRs exercise of its assessment powers.

The BIR, however, did not initiate any assessment for deficiency capital gains tax.78
Since more than a decade have lapsed from the filing of petitioner's return, the BIR
can no longer assess petitioner for deficiency capital gains taxes, if petitioner is
later found to have capital gains tax liabilities in excess of the amount claimed for
refund.

The Court of Tax Appeals should not be expected to perform the BIR's duties of
assessing and collecting taxes whenever the BIR, through neglect or oversight, fails
to do so within the prescriptive period allowed by law.

DISPOSITION:
 BIR is ordered to refund petitioner SMI-Ed Philippines Technology, Inc. the
amount of 5% final tax paid to the BIR, less the 6% capital gains tax on the
sale of petitioner SMI-Ed Philippines Technology, Inc. 's land and building.
In view of the lapse of the prescriptive period for assessment, any capital
gains tax accrued from the sale of its land and building that is in excess of
the 5% final tax paid to the Bureau of Internal Revenue may no longer be
recovered from petitioner SMI-Ed Philippines Technology, Inc.

SMI-ED Technology v. CIR

G.R. No. 175410
November 12, 2014

Facts:

In an action for the refund of taxes allegedly erroneously paid, the Court of Tax
Appeals may determine whether there are taxes that should have been paid in lieu
of the taxes paid. Determining the proper category of tax that should have been
paid is not an assessment. It is incidental to determining whether there should be a
refund.

A Philippine Economic Zone Authority (PEZA)-registered corporation that has never

commenced operations may not avail the tax incentives and preferential rates given
to PEZA-registered enterprises. Such corporation is subject to ordinary tax rates
under the National Internal Revenue Code of 1997.

This is a petition for review1 on certiorari of the November 3, 2006 Court of Tax
Appeals En Banc decision.2 It affirmed the Court of Tax Appeals Second Divisions
decision3 and resolution4 denying petitioner SMI-Ed Philippines Technology, Inc.s
(SMI-Ed Philippines) claim for tax refund.5

SMI-Ed Philippines is a PEZA-registered corporation authorized "to engage in the

business of manufacturing ultra high-density microprocessor unit package."6

After its registration on June 29, 1998, SMI-Ed Philippines constructed buildings and
purchased machineries and equipment.7 As of December 31, 1999, the total cost of
the properties amounted to P3,150,925,917.00.8

SMI-Ed Philippines "failed to commence operations."9 Its factory was temporarily

closed, effective October 15, 1999. On August 1, 2000, it sold its buildings and
some of its installed machineries and equipment to Ibiden Philippines, Inc., another
PEZA-registered enterprise, for 2,100,000,000.00 (P893,550,000.00). SMI-Ed
Philippines was dissolved on November 30, 2000.10

In its quarterly income tax return for year 2000, SMI-Ed Philippines subjected the
entire gross sales of itsproperties to 5% final tax on PEZA registered corporations.
SMI-Ed Philippines paid taxes amounting to P44,677,500.00.11

On February 2, 2001, after requesting the cancellation of its PEZA registration and
amending its articles of incorporation to shorten its corporate term, SMI-Ed
Philippines filed an administrative claim for the refund of P44,677,500.00 with the
Bureauof Internal Revenue (BIR). SMIEd Philippines alleged that the amountwas
erroneously paid. It also indicated the refundable amount in its final income tax
return filed on March 1, 2001. It also alleged that it incurred a net loss of
P2,233,464,538.00.12
The BIR did not act on SMI-Ed Philippines claim, which prompted the latter to file a
petition for reviewbefore the Court of Tax Appeals on September 9, 2002.13

The Court of Tax Appeals Second Division denied SMI-Ed Philippines claim for refund
in the decision dated December 29, 2004.14

The Court of Tax Appeals Second Division found that SMI-Ed Philippines
administrative claim for refund and the petition for review with the Court of Tax
Appeals were filed within the two-year prescriptive period.15 However, fiscal
incentives given to PEZA-registered enterprises may be availed only by PEZA-
registered enterprises that had already commenced operations.16 Since SMI-Ed
Philippines had not commenced operations, it was not entitled to the incentives of
either the income tax holiday or the 5% preferential tax rate.17 Payment of the 5%
preferential tax amounting to P44,677,500.00 was erroneous.18

After finding that SMI-Ed Philippines sold properties that were capital assets under
Section 39(A)(1) of the National Internal Revenue Code of 1997, the Court of Tax
Appeals Second Division subjected the sale of SMIEd Philippines assets to 6%
capital gains tax under Section 27(D)(5) of the same Code and Section 2 of Revenue
Regulations No. 8-98.19 It was found liable for capital gains tax amounting to
P53,613,000.00.20 Therefore, SMIEd Philippines must still pay the balance of
P8,935,500.00 as deficiency tax,21 "which respondent should perhaps look into."22
The dispositive portion of the Court of Tax Appeals Second Divisions decision reads:

WHEREFORE, premises considered, the instant petition is hereby DENIED.

SO ORDERED.23

The Court of Tax Appeals denied SMI-Ed Philippines motion for reconsideration in its
June 15, 2005 resolution.24

On July 17, 2005, SMI-Ed Philippines filed a petition for review before the Court of
Tax Appeals En Banc.25 It argued that the Court of Tax Appeals Second Division
erroneously assessed the 6% capital gains tax on the sale of SMI-Ed Philippines
equipment, machineries, and buildings.26 It also argued that the Court of Tax
Appeals Second Division cannot make an assessment at the first instance.27 Even if
the Court of Tax Appeals Second Division has such power, the period to make an
assessment had already prescribed.28

In the decision promulgated on November 3, 2006, the Court of Tax Appeals En

Banc dismissed SMI-Ed Philippines petition and affirmed the Court of Tax Appeals
Second Divisions decision and resolution.29 The dispositive portion of the Court of
Tax Appeals En Bancs decision reads:

WHEREFORE, finding no reversible error to reverse the assailed Decision

promulgated on December 29, 2004 and the Resolution dated June 15, 2005, the
instant petition for review is hereby DISMISSED. Accordingly, the assailed Decision
and Resolution are hereby AFFIRMED. SO ORDERED.30

SMI-Ed Philippines filed a petition for review before this court on December 27,
2006,31 praying for the grant of its claim for refund and the reversal of the Court of
Tax Appeals En Bancs decision.32

SMI-Ed Philippines assigned the following errors:

A. The honorable CTA En Banc grievously erred and acted beyond its jurisdiction
when it assessed for deficiency tax in the first instance.

B. Even assuming that the honorable CTA En Banc has the right to make an
assessment against the petitioner-appellant, it grievously erred in finding that the
machineries and equipment sold by the petitioner-appellant is subject to the six
percent (6%) capital gains tax under Section 27(D)(5) of the Tax Code.33

Petitioner argued that the Court of Tax Appeals has no jurisdiction to make an
assessment since its jurisdiction, with respect to the decisions of respondent, is
merely appellate.34 Moreover, the power to make assessment had already
prescribed under Section 203 of the National Internal Revenue Code of 1997 since
the return for the erroneous payment was filed on September 13, 2000. This is more
than three (3) years from the last day prescribed by law for the filing of the
return.35

Petitioner also argued that the Court of Tax Appeals En Banc erroneously subjected
petitioners machineries to 6% capital gains tax.36 Section 27(D)(5) of the National
Internal Revenue Code of 1997 is clear that the 6% capital gains tax on domestic
corporations applies only on the sale of lands and buildings and not tomachineries
and equipment.37 Since 1,700,000,000.00 of the 2,100,000,000.00 constituted
the consideration for the sale of petitioners machineries, only 400,000,000.00 or
P170,200,000.00 should be subjected to the 6% capital gains tax.38 Petitioner
should be liable only for P10,212,000.00.39 It should be entitled to a refund of
P34,464,500.00 after deducting P10,212,000.00 from the erroneously paid final tax
of P44,677,500.00.40

In its comment, respondent argued that the Court of Tax Appeals determination of
petitioners liability for capital gains tax was not an assessment. Such determination
was necessary to settle the question regarding the tax consequence of the sale of
the properties.41 This is clearly within the Court of Tax Appeals jurisdiction under
Section 7 of Republic Act No. 9282.42 Respondent also argued that "petitioner failed
to justify its claim for refund."43

The petition is meritorious.

Jurisdiction of the Court of Tax Appeals

The term "assessment" refers to the determination of amounts due from a person
obligated to make payments. In the context of national internal revenue collection,
it refers the determination of the taxes due from a taxpayer under the National
Internal Revenue Code of 1997.

The power and duty to assess national internal revenue taxes are lodged with the
BIR.44 Section 2 of the National Internal Revenue Code of 1997 provides:
SEC. 2. Powers and Duties of the Bureau of Internal Revenue. - The Bureau of
Internal Revenue shall be under the supervision and control of the Department of
Finance and its powers and duties shall comprehend the assessment and collection
ofall national internal revenue taxes, fees, and charges, and the enforcement of all
forfeitures, penalties, and fines connected therewith, including the execution of
judgments in all cases decided in its favor by the Court of Tax Appeals and the
ordinary courts. The Bureau shall give effect to and administer the supervisory and
police powers conferred to it by this Code or other laws. (Emphasis supplied) The
BIR is not mandated to make an assessment relative to every return filed with it. Tax
returns filed with the BIR enjoy the presumption that these are in accordance with
the law.45 Tax returns are also presumed correct since these are filed under the
penalty of perjury.46 Generally, however, the BIR assesses taxes when it appears,
after a return had been filed, that the taxes paid were incorrect,47 false,48 or
fraudulent.49 The BIR also assesses taxes when taxes are due but no return is
filed.50 Thus:

SEC. 6. Power of the Commissioner to Make assessments and Prescribe additional

Requirements for Tax Administration and Enforcement.

(A) Examination of Returns and Determination of Tax Due. - After a return has been
filed as required under the provisions of this Code, the Commissioner or his duly
authorized representative may authorize the examination of any taxpayer and the
assessment of the correct amount of tax: Provided, however; That failure to file a
return shall not prevent the Commissioner from authorizing the examination of any
taxpayer.The tax or any deficiency tax so assessed shall be paid upon notice and
demand from the Commissioner or from his duly authorized representative.

....

SEC. 222. Exceptions as to Period of Limitation of Assessment and Collection of

Taxes.

(a) In the case of a false or fraudulent return with intent to evade tax or of failure to
file a return, the tax may be assessed, or a preceeding in court for the collection of
such tax may be filed without assessment, at any time within ten (10) years after
the discovery of the falsity, fraud or omission: Provided, That in a fraud assessment
which has become final and executory, the fact of fraud shall be judicially taken
cognizance of in the civil or criminal action for the collection thereof. (Emphasis
supplied)

The Court of Tax Appeals has no powerto make an assessment at the first instance.
On matters such as tax collection, tax refund, and others related to the national
internal revenue taxes, the Court of Tax Appeals jurisdiction is appellate in nature.

Section 7(a)(1) and Section 7(a)(2) of Republic Act No. 1125,51 as amended by
Republic Act No. 9282,52 provide that the Court of Tax Appeals reviews decisions
and inactions of the Commissioner of Internal Revenue in disputed assessments and
claims for tax refunds. Thus: SEC. 7. Jurisdiction.- The CTA shall exercise:

a. Exclusive appellate jurisdiction toreview by appeal, as herein provided:

1. Decisions of the Commissioner of Internal Revenue in cases involving disputed

assessments, refunds of internal revenue taxes, fees or other charges, penalties in
relation thereto, or other matters arising under the National Internal Revenue or
other laws administered by the Bureau of Internal Revenue;

2. Inaction by the Commissioner of Internal Revenue in cases involving disputed

assessments, refunds of internal revenue taxes, fees or other charges, penalties in
relations thereto, or other matters arising under the National Internal Revenue Code
or other laws administered by the Bureau of Internal Revenue, where the National
Internal Revenue Code provides a specific period of action, in which case the
inaction shall be deemed a denial[.] (Emphasis supplied) Based on these provisions,
the following must be present for the Court of Tax Appeals to have jurisdiction over
a case involving the BIRs decisions or inactions:

a) A case involving any of the following:

i. Disputed assessments;
ii. Refunds of internal revenue taxes, fees, or other charges, penalties in relation
thereto; and

iii. Other matters arising under the National Internal Revenue Code of 1997.

b) Commissioner of Internal Revenues decision or inaction in a case submitted to

him or her

Thus, the BIR first has to make an assessment of the taxpayers liabilities. When the
BIR makes the assessment, the taxpayer is allowed to dispute that assessment
before the BIR. If the BIR issues a decision that is unfavorable to the taxpayer or if
the BIR fails to act on a dispute brought by the taxpayer, the BIRs decision or
inaction may be brought on appeal to the Court of Tax Appeals. The Court of Tax
Appeals then acquires jurisdiction over the case.

When the BIRs unfavorable decision is brought on appeal to the Court of Tax
Appeals, the Court of Tax Appeals reviews the correctness of the BIRs assessment
and decision. In reviewing the BIRs assessment and decision, the Court of Tax
Appeals had to make its own determination of the taxpayers tax liabilities. The
Court of Tax Appeals may not make such determination before the BIR makes its
assessment and before a dispute involving such assessment is brought to the Court
of Tax Appeals on appeal.

The Court of Tax Appeals jurisdiction is not limited to cases when the BIR makes an
assessment or a decision unfavorable to the taxpayer. Because Republic Act No.
112553 also vests the Court of Tax Appeals with jurisdiction over the BIRs inaction
on a taxpayers refund claim, there may be instances when the Court of Tax Appeals
has to take cognizance of cases that have nothing to do with the BIRs assessments
or decisions. When the BIR fails to act on a claim for refund of voluntarily but
mistakenly paid taxes, for example, there is no decision or assessment involved.

Taxes are generally self-assessed. They are initially computed and voluntarily paid
by the taxpayer. The government does not have to demand it. If the tax payments
are correct, the BIR need not make an assessment.
The self-assessing and voluntarily paying taxpayer, however, may later find that he
or she has erroneously paid taxes. Erroneously paid taxes may come in the form of
amounts thatshould not have been paid. Thus, a taxpayer may find that he or she
has paid more than the amount that should have been paid under the law.
Erroneously paid taxes may also come in the form of tax payments for the wrong
category of tax. Thus, a taxpayer may find that he or she has paid a certain kindof
tax that he or she is not subject to.

In these instances, the taxpayer may ask for a refund. If the BIR fails to act on the
request for refund, the taxpayer may bring the matter to the Court of Tax Appeals.

From the taxpayers self-assessment and tax payment up to his or her request for
refund and the BIRs inaction,the BIRs participation is limited to the receipt of the
taxpayers payment. The BIR does not make an assessment; the BIR issues no
decision; and there is no dispute yet involved. Since there is no BIR assessment yet,
the Court of Tax Appeals may not determine the amount of taxes due from the
taxpayer. There is also no decision yet to review. However, there was inaction on
the part of the BIR. That inaction is within the Court of Tax Appeals jurisdiction.

In other words, the Court of Tax Appeals may acquire jurisdiction over cases even if
they do not involve BIR assessments or decisions.

In this case, the Court of Tax Appeals jurisdiction was acquired because petitioner
brought the case on appeal before the Court of Tax Appeals after the BIR had failed
to act on petitioners claim for refund of erroneously paid taxes. The Court of Tax
Appeals did not acquire jurisdiction as a result of a disputed assessment of a BIR
decision.

Petitioner argued that the Court of Tax Appeals had no jurisdiction to subject it to
6% capital gains tax or other taxes at the first instance. The Court of Tax Appeals
has no power to make an assessment.

As earlier established, the Court of Tax Appeals has no assessment powers. In

stating that petitioners transactions are subject to capital gains tax, however, the
Court of Tax Appeals was not making an assessment. It was merely determining the
proper category of tax that petitioner should have paid, in view of its claim that it
erroneously imposed upon itself and paid the 5% final tax imposed upon PEZA-
registered enterprises.

The determination of the proper category of tax that petitioner should have paid is
an incidental matter necessary for the resolution of the principal issue, which is
whether petitioner was entitled to a refund.54

The issue of petitioners claim for tax refund is intertwined with the issue of the
proper taxes that are due from petitioner. A claim for tax refund carries the
assumption that the tax returns filed were correct.55 If the tax return filed was not
proper, the correctness of the amount paid and, therefore, the claim for refund
become questionable. In that case, the court must determine if a taxpayer claiming
refund of erroneously paid taxes is more properly liable for taxes other than that
paid.

In South African Airways v. Commissioner of Internal Revenue,56 South African

Airways claimed for refund of its erroneously paid 2% taxes on its gross Philippine
billings. This court did not immediately grant South Africans claim for refund. This is
because although this court found that South African Airways was not subject to the
2% tax on its gross Philippine billings, this court also found that it was subject to
32% tax on its taxable income.57

In this case, petitioners claim that it erroneously paid the 5% final tax is an
admission that the quarterly tax return it filed in 2000 was improper. Hence, to
determine if petitioner was entitled to the refund being claimed, the Court of Tax
Appeals has the duty to determine if petitioner was indeed not liable for the 5% final
tax and, instead, liable for taxes other than the 5% final tax. As in South African
Airways, petitioners request for refund can neither be granted nor denied outright
without such determination.58

If the taxpayer is found liable for taxes other than the erroneously paid 5% final tax,
the amount of the taxpayers liability should be computed and deducted from the
refundable amount.

Any liability in excess of the refundable amount, however, may not be collected in a
case involving solely the issue of the taxpayers entitlement to refund. The question
of tax deficiencyis distinct and unrelated to the question of petitioners entitlement
to refund. Tax deficiencies should be subject to assessment procedures and the
rules of prescription. The court cannot be expected to perform the BIRs duties
whenever it fails to do so either through neglect or oversight. Neither can court
processes be used as a tool to circumvent laws protecting the rights of taxpayers.

II

Petitioners entitlement to benefits given to PEZA-registered enterprises

Petitioner is not entitled to benefits given to PEZA-registered enterprises, including

the 5% preferential tax rate under Republic Act No. 7916 or the Special Economic
Zone Act of 1995. This is because it never began its operation.

Essentially, the purpose of Republic Act No. 7916 is to promote development and
encourage investments and business activities that will generate employment.59
Giving fiscal incentives to businesses is one of the means devised to achieve this
purpose. It comes with the expectation that persons who will avail these incentives
will contribute to the purposes achievement. Hence, to avail the fiscal incentives
under Republic Act No. 7916, the law did not say that mere PEZA registration is
sufficient.

Republic Act No. 7916 or The Special Economic Zone Act of 1995 provides:

SEC. 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
same benefits provided for in the Export Development Act of 1994.
SEC. 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
tothe national government. This five percent (5%) shall be shared and distributed as
follows:

a. Three percent (3%) to the national government;

b. One percent (1%) to the localgovernment units affected by the declaration of the
ECOZONE inproportion to their population, land area, and equal sharing factors; and

c. One percent (1%) for the establishment of a development fund to be utilized for
the development of municipalities outside and contiguous to each ECOZONE:
Provided, however, That the respective share of the affected local government units
shall be determined on the basis of the following formula:

1. Population - fifty percent (50%);

2. Land area - twenty-five percent (25%); and

3. Equal sharing - twenty-five percent (25%). (Emphasis supplied)

Based on these provisions, the fiscal incentives and the 5% preferential tax rate are
available only to businesses operating within the Ecozone.60 A business is
considered in operation when it starts entering into commercial transactions that
are not merely incidental to but are related to the purposes of the business. It is
similar to the definition of "doing business," as applied in actions involvingthe right
of foreign corporations to maintain court actions. In Mentholatum Co. Inc., et al. v.
Mangaliman, et al.,61 this court said that the terms "doing" or "engaging in" or
"transacting" business":
. . . impl[y] a continuity of commercial dealings and arrangements, and
contemplates, to that extent, the performance of acts or works or the exercise of
some of the functions normally incident to, and in progressive prosecution of, the
purpose and object of its organization.62 Petitioner never started its operations
since its registration on June 29, 199863 because of the Asian financial crisis.64
Petitioner admitted this.65 Therefore, it cannot avail the incentives provided under
Republic Act No. 7916. It is not entitled to the preferential tax rate of 5% on gross
income in lieu of all taxes. Because petitioner is not entitled to a preferential rate, it
is subject to ordinary tax rates under the National Internal Revenue Code of 1997.

III

Imposition of capital gains tax

The Court of Tax Appeals found that petitioners sale of its properties is subject to
capital gains tax.

For petitioners properties to be subjected to capital gains tax, the properties must
form part ofpetitioners capital assets.

Section 39(A)(1) of the National Internal Revenue Code of 1997 defines "capital
assets":

SEC. 39. Capital Gains and Losses. -

(A) Definitions.- As used in this Title -

(1) Capital Assets.- the term capital assets means property held by the taxpayer
(whether or not connected with his trade or business), but does not include stock in
trade of the taxpayer or other property of a kind which would properly be included
in the inventory of the taxpayer if on hand at the close of the taxable year, or
property held by the taxpayer primarily for sale to customers in the ordinary course
of his trade orbusiness, or property used in the trade or business, of a character
which is subject to the allowance for depreciation provided in Subsection (F) of
Section 34; or real property used in trade or business of the taxpayer. (Emphasis
supplied) Thus, "capital assets" refers to taxpayers property that is NOT any of the
following:

1. Stock in trade;

2. Property that should be included inthe taxpayers inventory at the close of the
taxable year;

3. Property held for sale in the ordinary course of the taxpayers business;

4. Depreciable property used in the trade or business; and

5. Real property used in the trade or business.

The properties involved in this case include petitioners buildings, equipment, and
machineries. They are not among the exclusions enumerated in Section 39(A)(1) of
the National Internal Revenue Code of 1997. None of the properties were used in
petitioners trade or ordinary course of business because petitioner never
commenced operations. They were not part of the inventory. None of themwere
stocks in trade. Based on the definition of capital assets under Section 39 of the
National Internal Revenue Code of 1997, they are capital assets.

Respondent insists that since petitioners machineries and equipment are classified
as capital assets, their sales should be subject to capital gains tax. Respondent is
mistaken.

In Commissioner of Internal Revenue v. Fortune Tobacco Corporation,66 this court

said:
The rule in the interpretation of tax laws is that a statute will not be construed as
imposing a tax unless it does so clearly, expressly, and unambiguously. A tax cannot
be imposed without clear and express words for that purpose. Accordingly, the
general rule of requiring adherence to the letter in construing statutes applies with
peculiar strictness to tax laws and the provisions of a taxing act are not to be
extended by implication. In answering the question of who is subject to tax statutes,
it is basic that in case of doubt, such statutes are to be construed most strongly
against the government and in favor of the subjects or citizens because burdens are
not to be imposed nor presumed to be imposed beyond what statutes expressly and
clearly import. As burdens, taxes should not be unduly exacted nor assumed
beyond the plain meaning of the tax laws.67 (Citations omitted)

Capital gains of individuals and corporations from the sale of real properties are
taxed differently. Individuals are taxed on capital gains from sale of all real
properties located in the Philippines and classified as capital assets. Thus:

SEC. 24. Income Tax Rates.

....

(D) Capital Gains from Sale of Real Property.

(1) In General. - The provisions of Section 39(B) notwithstanding, a final tax of six
percent (6%) based on the gross selling price or current fair market value as
determined in accordance with Section 6(E) of this Code, whichever is higher, is
hereby imposed upon capital gains presumed to have been realized from the sale,
exchange, or other disposition of real property located in the Philippines, classified
as capital assets, including pacto de retro sales and other forms of conditional sales,
by individuals, including estates and trusts: Provided, That the tax liability, if any, on
gains from sales or other dispositions of real property to the government or any of
its political subdivisions or agencies or to government-owned or controlled
corporations shall be determined either under Section 24 (A) or under this
Subsection, at the option of the taxpayer.68 (Emphasis supplied)

For corporations, the National Internal Revenue Code of 1997 treats the sale of land
and buildings, and the sale of machineries and equipment, differently. Domestic
corporations are imposed a 6% capital gains tax only on the presumed gain realized
from the sale of lands and/or buildings. The National Internal Revenue Code of 1997
does not impose the 6% capital gains tax on the gains realized from the sale of
machineries and equipment. Section 27(D)(5) of the National Internal Revenue Code
of 1997 provides:

SEC. 27. Rates of Income tax on Domestic Corporations. -

....

(D) Rates of Tax on Certain Passive Incomes. -

....

(5) Capital Gains Realized from the Sale, Exchange or Disposition of Lands and/or
Buildings. - A final tax of six percent (6%) is hereby imposed on the gain presumed
to have been realized on the sale, exchange or disposition of lands and/or buildings
which are not actually used in the business of a corporation and are treated as
capital assets, based on the gross selling price of fair market value as determined in
accordance with Section 6(E) of this Code, whichever is higher, of such lands and/or
buildings. (Emphasis supplied)

Therefore, only the presumed gain from the sale of petitioners land and/or building
may be subjected to the 6% capital gains tax. The income from the sale of
petitioners machineries and equipment is subject to the provisions on normal
corporate income tax.

To determine, therefore, if petitioner is entitled to refund, the amount of capital

gains tax for the sold land and/or building of petitioner and the amount of corporate
income tax for the sale of petitioners machineries and equipment should be
deducted from the total final tax paid. Petitioner indicated, however, in its March 1,
2001 income tax return for the 11-month period ending on November 30, 2000 that
it suffered a net loss of P2,233,464,538.00.69 This declaration was made under the
pain of perjury. Section 267 of the National Internal Revenue Code of 1997 provides:

SEC. 267. Declaration under Penalties of Perjury. - Any declaration, return and other
statement required under this Code, shall, in lieu of an oath, contain a written
statement that they are made under the penalties of perjury. Any person who
willfully files a declaration, return or statement containing information which is not
true and correct as to every material matter shall, upon conviction, be subject to
the penalties prescribed for perjury under the Revised Penal Code. Moreover, Rule
131, Section 3(ff) of the Rules of Court provides for the presumption that the law
has been obeyed unless contradicted or overcome by other evidence, thus:

SEC. 3. Disputable presumptions. The following presumptions are satisfactory if

uncontradicted, but may be contradicted and overcome by other evidence:

....

(ff) That the law has been obeyed;

The BIR did not make a deficiency assessment for this declaration. Neither did the
BIR dispute this statement in its pleadings filed before this court. There is, therefore,
no reason todoubt the truth that petitioner indeed suffered a net loss in 2000.

Since petitioner had not started its operations, it was also not subject to the
minimum corporate income tax of 2% on gross income.70 Therefore, petitioner is
not liable for any income tax.

IV

Prescription
Section 203 of the National Internal Revenue Code of 1997 provides that as a
general rule, the BIR has three (3) years from the last day prescribed by law for the
filing of a return to make an assessment. If the return is filed beyond the last day
prescribed by law for filing, the three-year period shall run from the actual date of
filing. Thus:

SEC. 203. Period of Limitation Upon Assessment and Collection. - Except as provided
in Section 222, internal revenue taxes shall be assessed within three (3) years after
the last day prescribed by law for the filing of the return, and no proceeding in court
without assessment for the collection of such taxes shall be begun after the
expiration of such period: Provided, That in a case where a return is filed beyond the
period prescribed by law, the three (3)-year period shall be counted from the day
the return was filed. For purposes of this Section, a return filed before the last day
prescribed by law for the filing thereof shall be considered as filed on such last day.

This court said that the prescriptive period to make an assessment of internal
revenue taxes is provided "primarily to safeguard the interests of taxpayers from
unreasonable investigation."71 This court explained in Commissioner of Internal
Revenue v. FMF Development Corporation72 the reason behind the provisions on
prescriptive periods for tax assessments: Accordingly, the government must assess
internal revenue taxes on time so as not to extend indefinitely the period of
assessment and deprive the taxpayer of the assurance that it will no longer be
subjected to further investigation for taxes after the expiration of reasonable period
of time.73

Rules derogating taxpayers right against prolonged and unscrupulous

investigations are strictly construed against the government.74

[T]he law on prescription should beinterpreted in a way conducive to bringing about

the beneficent purpose of affording protection to the taxpayer within the
contemplation of the Commission which recommended the approval of the law. To
the Government, its tax officers are obliged to act promptlyin the making of
assessment so that taxpayers, after the lapse of the period of prescription, would
have a feeling of security against unscrupulous tax agents who will always try to
find an excuse to inspect the books of taxpayers, not to determine the latters real
liability, but to take advantage of a possible opportunity to harass even law-abiding
businessmen. Without such legal defense, taxpayers would be open season to
harassment by unscrupulous tax agents.75
Moreover, in Commissioner of Internal Revenue v. BF Goodrich Phils.:76

For the purpose of safeguarding taxpayers from any unreasonable examination,

investigation or assessment, our tax law provides a statute of limitations in the
collection of taxes. Thus, the law on prescription, being a remedial measure, should
be liberally construed in order to afford such protection. As a corollary, the
exceptions to the law on prescription should perforce be strictly construed[.]

....

. . . . Such instances of negligence or oversight on the part of the BIR cannot

prejudice taxpayers, considering that the prescriptive period was precisely intended
to give them peace of mind.77 (Citation omitted)

The BIR had three years from the filing of petitioners final tax return in 2000 to
assess petitioners taxes. Nothing stopped the BIR from making the correct
assessment. The elevation of the refund claim with the Court of Tax Appeals was not
a bar against the BIRs exercise of its assessment powers.

The BIR, however, did not initiate any assessment for deficiency capital gains tax.78
Since more than a decade have lapsed from the filing of petitioner's return, the BIR
can no longer assess petitioner for deficiency capital gains taxes, if petitioner is
later found to have capital gains tax liabilities in excess of the amount claimed for
refund.

The Court of Tax Appeals should not be expected to perform the BIR's duties of
assessing and collecting taxes whenever the BIR, through neglect or oversight, fails
to do so within the prescriptive period allowed by law.

WHEREFORE, the Court of Tax Appeals' November 3, 2006 decision is SET ASIDE.
The Bureau of Internal Revenue is ordered to refund petitioner SMI-Ed Philippines
Technology, Inc. the amount of 5% final tax paid to the BIR, less the 6% capital
gains tax on the sale of petitioner SMI-Ed Philippines Technology, Inc. 's land and
building. In view of the lapse of the prescriptive period for assessment, any capital
gains tax accrued from the sale of its land and building that is in excess of the 5%
final tax paid to the Bureau of Internal Revenue may no longer be recovered from
petitioner SMI-Ed Philippines Technology, Inc.

SO ORDERED.