G.R. No. 148339 - Lucena Grand Central Terminal Inc. vs. JAC Liner Inc.

San Roque Power Corporation, a VAT-registered taxpayer, filed administrative claims for refund/credit of unutilized input VAT attributable to its zero-rated sales of electricity to National Power Corporation (NPC).
The petitioner originally secured a zero-rating on its electricity sales effective from 14 January 2004 up to 31 December 2004.
Two separate administrative claims were submitted:

Pursuant to the inaction of the Commissioner of Internal Revenue (CIR) in resolving its claim, San Roque later sought judicial relief by filing petitions for review before the Court of Tax Appeals (CTA).

On 30 March 2006 (CTA Case No. 7424) seeking refund/credit for the first administrative claim.
On 20 June 2006 (CTA Case No. 7492) for the second administrative claim.

These filings were made prior to the Supreme Court’s pronouncement in Commissioner of Internal Revenue v. Aichi Forging Company of Asia, Inc. (Aichi) yet raised questions regarding the applicability of the 120-day and 30-day periods as provided in Section 112(D) of the National Internal Revenue Code (NIRC).
The CTA Division, after trial, partially granted the refund claim by ordering the CIR to refund or issue a tax credit certificate in the total amount of ₱29,931,505.18.
Subsequently, the CTA En Banc dismissed the judicial claims on the ground of prematurity, basing its decision on the non-observance of the mandatory 120-day period for administrative resolution as well as the ensuing 30-day period for appeal.

The Aichi ruling clarified that the 120-day and 30-day periods provided in Section 112(D) are mandatory and jurisdictional, precluding the simultaneous filing of both administrative and judicial claims outside of the prescribed timelines.
San Roque Power Corporation contended that prior to Aichi, prevailing interpretations of CTA rules allowed filing judicial claims within the two-year prescriptive period.
The petitioner also raised concerns regarding the retroactive application of the Aichi ruling, arguing that it altered a supposedly established procedural rule and impaired vested rights.
The petitioner’s reliance on certain CTA decisions, which were favorable to filing premature claims, is rebutted by the Supreme Court’s assertion that CTA decisions are not binding precedents for altering the clear statutory scheme set by Section 112(D) of the NIRC.

Whether the filing of judicial claims before the full expiration of the 120-day administrative period constitutes a violation of the mandatory and jurisdictional period prescribed in Section 112(D) of the NIRC.
Whether the petitioner’s reliance on pre-Aichi CTA interpretations that permitted filing judicial claims within the two-year prescriptive period is legally tenable.
Whether the retroactive application of the Aichi ruling, which strictly enforces the 120-day/30-day period, impairs any vested rights of the taxpayer.
Whether the exception provided by BIR Ruling No. DA-489-03—shielding taxpayers who filed their claims during the window period from December 10, 2003, up to October 6, 2010—applies to the case even if not explicitly invoked by the petitioner.