G.R. No. 187485 - Commissioner of Internal Revenue vs. San Roque Power Corp.

San Roque Power Corporation (“San Roque”) is a BOI-registered pioneer domestic corporation formed in October 1997 to build and operate a hydroelectric power plant under a Power Purchase Agreement with the National Power Corporation.
In 2001, San Roque purchased capital goods and services for the project, resulting in unutilized input VAT of ₱559,709,337.54, later amended to ₱560,200,283.14.
San Roque filed separate administrative refund claims for each 2001 quarter (July 10, 2001 to May 9, 2002) and amended them on March 28, 2003 (totaling ₱560,200,283.14).
On April 10, 2003 (13 days after the March 28 amended claims), San Roque filed a Petition for Review with the CTA Second Division (CTA Case No. 6647).
The CTA Second Division initially denied the claim (March 8, 2006), then partially granted it on reconsideration (Amended Decision, November 29, 2007), awarding ₱483,797,599.65.
The Commissioner petitioned the CTA En Banc, which on March 25, 2009 affirmed the Second Division’s Amended Decision and on April 24, 2009 denied reconsideration.

Taganito Mining Corporation (“Taganito”) is a BOI-registered nickel ore exporter, VAT-registered, with 2005 zero-rated sales of ₱1,446,854,034.68 and total input VAT claimed of ₱8,365,664.38.
It filed original QVAT returns for 2005 and amended them on July 20 and October 18, 2006.
On November 14, 2006, Taganito filed its administrative claim for ₱8,365,664.38 (later corrected to cover 2005).
On February 17, 2007 (92 days later), it filed a Petition for Review with the CTA Second Division (CTA Case No. 7574).
The Second Division granted a partial refund of ₱8,249,883.33 (January 8, 2010) and denied reconsideration (April 7, 2010).
The CTA En Banc reversed and dismissed the claim as prematurely filed (December 8, 2010), denying reconsideration (March 14, 2011).

Philex Mining Corporation (“Philex”) filed its Original QVAT Return for Q3 2005 on October 21, 2005 and amended it on December 1, 2005.
It filed an administrative claim for refund/credit of ₱23,956,732.44 on March 20, 2006.
On October 17, 2007 (426 days after the administrative claim), Philex filed a Petition for Review with the CTA Second Division (CTA Case No. 7687).
The Second Division dismissed the petition as barred by prescription (July 20, 2009) and denied reconsideration (November 10, 2009).
The CTA En Banc affirmed the dismissal on December 3, 2010, ruling that Philex filed too late after the 120+30-day period.

Whether San Roque’s judicial claim (filed 13 days after its administrative claim) was prematurely filed, depriving the CTA of jurisdiction for failure to comply with the 120-day waiting period under Section 112(D) of the NIRC.
Whether Taganito’s judicial claim (filed 92 days after its administrative claim) violated the mandatory 120+30-day period, rendering its petition premature and beyond CTA jurisdiction.
Whether Philex’s judicial claim (filed 426 days after its administrative claim) was filed out of time, beyond the 30 days from deemed denial, and thus barred.