Reckoning Limitation Period From Subsequent Manual Filing

Reckoning Limitation Period From Subsequent Manual Filing Date When Online GST Refund Application Was Already Acknowledged Is Illegal

Issue

Whether tax authorities can reckon the limitation period from a subsequent manual filing date under Rule 97A to reject a GST refund claim as time-barred, when the online refund application was filed and acknowledged within the statutory two-year period.

Facts

The petitioner-assessee, registered under the CGST/SGST Act, filed an online application for a tax refund for the period 2017-18.
The online refund application was submitted within the statutory two-year limitation period and was duly acknowledged by the Department on February 12, 2019.
The Assessing Officer (AO) processed the refund claim by invoking Rule 97A of the CGST/SGST Rules, 2017.
The AO treated the subsequent manual submission on November 14, 2019, as the relevant date for determining limitation, thereby rejecting the refund claim as time-barred (Ext.P2).
The first appellate authority dismissed the appeal and upheld the rejection order (Ext.P1).
The petitioner filed a writ petition challenging the rejection order despite the availability of an alternative remedy, given the prolonged pendency and legal error.

Decision

The High Court held that the writ petition was maintainable and warranted intervention despite appellate remedies due to the arbitrary application of Rule 97A.
It was observed that Rule 97A merely enables manual filing in addition to electronic mode, as evidenced by the word “include” in the provision.
The Court held that since the online refund application had already been acknowledged on February 12, 2019, reckoning limitation from the subsequent manual filing date was illegal and arbitrary.
The refund claim ought to have been considered with reference to the acknowledged online filing date.
Consequently, the writ petition was allowed, Ext.P2 was set aside, and the 1st respondent was directed to process the refund application in accordance with law expeditiously in favor of the assessee.

Key Takeaways

Primary Date for Limitation: When an online GST refund application is duly filed and acknowledged within time, that acknowledgment date governs limitation.
Scope of Rule 97A: Rule 97A provides an additional enabling option for manual filing; it does not invalidate or override a timely electronic filing.
Arbitrary Rejection Overruled: Tax authorities cannot artificially shift the relevant limitation date to a subsequent physical/manual submission when electronic receipt is acknowledged.

HIGH COURT OF KERALA

MSD Pharmaceuticals (P.) Ltd.

Assistant Commissioner

Harisankar V. Menon, J.

WP(C) NO. 7284 OF 2023

JULY 10, 2026

Karthik S. Nair and Prabhakaran P.M., Advs. for the Petitioner. Mohammed Shafi K., Govt. Pleader for the Respondent.

JUDGMENT

1. The petitioner is an assesee under the provisions of the Central Goods and Services Tax/ State Goods and Services Tax Act, 2017. The dispute in this writ petition is with reference to an application seeking refund filed under Section 54 of the Central Goods and Services Tax Act, 2017 (hereinafter referred to as ‘the Act’). According to the petitioner, the refund application has been presented within the statutory prescription of two years as evidenced by Ext.P12 receipt, as per which, the application is filed admittedly on 12.02.2019. Straightaway it may be noticed that the application acknowledged by Ext.P12 is the online application filed under the statute. However, this application has been processed by the impugned order at Ext.P2 with reference to the mandate under Rule 97A of the Central Goods and Services Tax Rules, 2017 (hereinafter referred to as ‘the Rules’) concluding that the petitioner has chosen to file the “hard copy” of the application only on 14.11.2019, which is well beyond the statutory prescription of two years. Stating this reason, the application seeking refund with respect to the assessment year 2017-18 has been rejected by the impugned order at Ext.P2.

2. Heard Sri.Karthik S.Nair, the learned counsel for the petitioner, as well as Sri.Mohammed Shafi K., the learned Government Pleader.

3. The learned Government Pleader, however, submits that the order at Ext.P2 was challenged by the petitioner by filing an appeal under Section 107 of the Act, and that the Appellate Authority has also rejected the same by Ext.P1. Therefore, according to the learned Government Pleader, it is for the petitioner to file a further appeal to the Tribunal under Section 112 of the Act.

4. Sri.Karthik would, however, point out that the order of the Appellate Authority at Ext.P1 is also a non-speaking one, insofar as the contention with reference to the online filing of the refund application, as has been specifically raised in ground Nos.2 and 3, has not been considered by the Appellate Authority.

5. In any event, I am of the opinion that, since the issue is with reference to the processing of a refund application, which appears to have been rejected with reference to the mandate under Rule 97A, the question requires to be considered by this Court, since, admittedly, the writ petition has been pending consideration before this Court for more than three years. Even if an appeal has been preferred to the Tribunal, ultimately, the afore matter requires to be considered with reference to the mandate under Rule 97A, and if it is found that the matter requires to be reconsidered, the files requires to be remitted to the original authority.

6. Hence, even on the face of the provisions of Section 112 of the Act, this Court proceeds to consider the legality or otherwise of the findings contained in Ext.P2.

7. As already noticed, Ext.P2 has been issued only because Rule 97A provided for the filing of a manual application. Rule 97A of the Rules provides as under;

“97A. Manual filing and processing. – Notwithstanding anything contained in this Chapter, in respect of any process or procedure prescribed herein, any reference to electronic filing of an application, intimation, reply, declaration, statement or electronic issuance of a notice, order or certificate on the common portal shall, in respect of that process or procedure, include manual filing of the said application, intimation, reply, declaration, statement or issuance of the said notice, order or certificate in such Forms as appended to these rules.”

A reading of the afore provision would show that the rule making authority has only thought of providing that a manual application can also be presented with reference to a refund claim. This is made clear by use of the word “include” under Rule 97A. Therefore, merely for the reason that in tune with Rule 97A, the petitioner chose to file a manual refund application on 14.11.2019, I am of the opinion that the rejection of the application seeking refund was illegal and arbitrary. The application seeking refund ought to have been considered with reference to the online application admittedly acknowledged on 12.02.2019.

8. Hence, I am of the opinion that the matter requires a revisit at the hands of the 1^st respondent herein.

Therefore, this writ petition would stand allowed, setting aside Ext.P2. The 1^st respondent is directed to consider the refund application in accordance with law. The application requires to be processed and disposed of, as expeditiously as possible, at any rate, within a period of three months from the date of receipt of a copy of this judgment.