COMMISSIONER OF INTERNAL REVENUE VS.

SAN ROQUE POWER

CORPORATION
707 SCRA 66 | G.R. NO. 187485 | OCTOBER 8, 2013

Effect of Declaration of Unconstitutionality: OPERATIVE FACT DOCTRINE

CARPIO, J.

FACTS
In February 2013 the Court decided on the consolidated cases involving San Roque Power,
Taganito Mining and Philex Mining. The cases all involved the timely filing by the taxpayers of
their administrative claims with the Commissioner of Internal Revenue regarding their intent to
claim a tax refund. In the case of San Roque, the petitioner prematurely filed their judicial claims
without waiting for the 120-day period to lapse for the Commissioner to act on their
administrative claims; the respondent filed on April 10, 2003, a mere 13 days after it filed its
judicial claim.

San Roque claimed that the Court has invalidated BIR Ruling No. DA-489-03 and that there
should be an exemption with regards to the Operative Fact Doctrine through asserting that “the
BIR and the CTA in actual practice did not observe and did not require refund seekers to comply
with the 120+30 days period.” Thus, they prayed for the rule established in our February 12,
2013 decision be given only a prospective effect, arguing that “the manner by which the Bureau
of Internal Revenue and the Court of Tax Appeals actually treated the 120+30 day periods
constitutes an operative fact the effects and consequences of which cannot be erased or undone.”
ISSUE
Whether or not the San Roque Power Corporation’s justification of the application of the
Operative Fact Doctrine is valid.

HELD
No. San Roque’s justification of the application of the Operative Fact Doctrine is invalid because
under Section 246, taxpayers may rely upon a rule or ruling issued by the Commissioner from
the time the rule or ruling is issued up (BIR Ruling No. DA-489-03 dated February 10, 2003) to
its reversal by the Commissioner or this Court (Aichi doctrine dated October 6, 2010). Thus, in
this case, reversal is not given retroactive effect; the law has already prescribed in Section 246 of
the Tax Code how the doctrine of operative fact should be applied and there can be no invocation
of this doctrine other than what the law has specifically provided in the said provision.

In the case at bar, the rule or ruling subject of the operative fact doctrine is BIR Ruling No. DA-
489-03 dated December 10, 2003; and prior to this date, there is no such rule or ruling calling for
the application of the operative fact doctrine in Section 246. This clearly projects that being an
exemption of statutory taxation, Section 246 must be applied strictly against the taxpayer
claiming such exemption.

Thus, the Court granted the petition of the Commission one Internnal Revenue to deny the
tax refund or credit claim of San Roque Power Corporation.