High Court Remands ITC Mismatch Case (GSTR-2A vs 3B) on Condition of 10% Pre-deposit

By | January 12, 2026

High Court Remands ITC Mismatch Case (GSTR-2A vs 3B) on Condition of 10% Pre-deposit

Issue

  1. ITC Denial: Whether Input Tax Credit (ITC) can be denied due to a mismatch between GSTR-2A and GSTR-3B caused by technical glitches (lack of synchronization between GST portal and ICEGATE).

  2. Extended Limitation: Whether the Revenue can invoke the extended period of limitation under Section 74 (alleging fraud/suppression) when the discrepancy arose from a system error during the initial GST period (July 2017 – March 2018).

  3. Validity of Order: Whether an assessment order should be quashed if the assessee failed to reply on the merits of the allegation, relying only on legal arguments.

Facts

  • Period: July 2017 to March 2018 (Implementation phase of GST).

  • The Dispute: The petitioner claimed Input Tax Credit on IGST paid on imports. A mismatch occurred between the ITC claimed in GSTR-3B and the data reflected in GSTR-2A.

  • Reason for Mismatch: The assessee argued this was due to a technical glitch: the GST portal was not fully synchronized with the ICEGATE portal (Customs), preventing the auto-population of credit.

  • Show Cause Notice (SCN): The Department issued an SCN based on an audit report, invoking the extended period of limitation under Section 74.

  • Assessee’s Error: In their reply to the SCN, the assessee focused solely on legal submissions (challenging the limitation period and clarity of notice) and failed to address the factual merits of the discrepancy.

  • Impugned Order: Consequently, the authority confirmed the demand, noting there was no factual rebuttal.

Decision

  • Assessee’s Failure: The High Court noted that the challenge to the order was initially weak because the assessee had not provided a reply on the merits, leaving the authority with no option but to confirm the demand.

  • Remand for Justice: However, recognizing that the issue stemmed from the initial GST transition period and technical difficulties, the Court decided to give the assessee another opportunity to prove their case on facts.

  • Condition Imposed: The impugned order was quashed and the matter remitted back to the authority for fresh adjudication. This relief was granted subject to the condition that the assessee deposits 10% of the disputed tax from their Electronic Cash Ledger within 30 days. [In favour of assessee/Matter remanded]

Key Takeaways

  • Reply on Merits is Mandatory: Relying solely on technical legal arguments (like “limitation period”) without explaining the factual discrepancy (the “why” behind the mismatch) is a risky strategy. Always address the core allegation.

  • Transitional Glitches: Courts are generally lenient regarding errors occurred during the initial phase of GST (2017-18), provided there is proof of technical glitches (like ICEGATE sync issues).

  • Pre-deposit for Remand: If an assessee bypasses the statutory appeal route and approaches the High Court directly due to a botched reply, the Court often imposes a pre-deposit condition (similar to the 10% required for statutory appeals) to ensure bona fides.

HIGH COURT OF MADRAS
Elgi Sauer Compressors Ltd.
v.
State Tax Officer*
C. Saravanan, J.
WP No. 13037 of 2025
W.M.P. No. 14551 of 2025
NOVEMBER  27, 2025
G. Vardini Karthik for the Petitioner. Ms. P.Selvi, Govt. Adv. (tax) for the Respondent.
ORDER
1. In this Writ Petition, the Petitioner has challenged the impugned order dated 05.02.2025 passed in GSTIN 33AACCE0460H1Z5/2017-18, whereby the demand proposed in show cause notice dated 16.08.2024 issued for the tax period July 2017 – March 2018 has been confirmed.
2.The Petitioner had given a reply to the show cause notice wherein the Petitioner has taken only a legal plea on the ground of finality and in view of the dropping of the proceedings initiated earlier in DRC – 01A dated 25.03.2022 and DRC-01 dated 25.04.2022.
3.The entire proceedings is in the background of an audit conducted on 28.02.2022, wherein certain discrepancies were pointed out in Pre-show cause notice in DRC-01A dated 25.03.2022 issued by the 3rd Respondent, followed by a DRC-01 dated 25.04.2022 and a communication dated 06.10.2023.
4.As far as the impugned order is concerned, pursuant to the show cause notice in DRC-01 dated 16.08.2024, the demand that has been confirmed is for a sum of Rs.1,64,02,442/- towards the tax and further amount towards interest under Section 50 and penalty under Section 74 of the respective GST enactments.
5.The Petitioner has now challenged the impugned order on the ground that there is no case available for invoking extended period of limitation under Section 74 of TNGST Act, and that the show cause notice that preceded the impugned order on 16.08.2024 is also unclear and is purely based on the audit report.
6.That apart, it is submitted that the dispute has arisen on account of mismatch between GSTR 2A and GSTR 3B. It is submitted that during the period in dispute, there was a technical glitch and that the GST portal was not fully synchronized with Icegate portal, therefore there were difficulties in claiming input tax credit on account of IGST Transaction. This aspect ought to have been part of the reply of the Petitioner to the show cause notice dated 16.08.2024 issued to the Petitioner.
7.Instead, the Petitioner has confined the reply to few legal submissions without any reference on the merits of the allegation and de-merits of the allegation in show cause notice in DRC-01 dated 16.08.2024. Therefore, the challenge to the impugned order passed by the Respondent cannot be countenanced as the Respondent was left with no other option, except to confirm the demand. It is also not open for the Petitioner to challenge the proceeding on the ground of limitation under Section 74 without appropriate reply on merits.
8.To appreciate whether indeed a case was made out or not for invoking extended period of limitation or not, the Petitioner should have given a proper reply on merits as well together and combine it with legal submissions on the law.
9.Since the Petitioner has approached this Court almost immediately after the impugned order came to be passed, the case is remitted back to the Respondent by quashing the impugned order, subject to the Petitioner depositing 10% of the disputed tax from the Petitioner’s Electronic Cash Register within a period of thirty (30) days from the date of receipt of a copy of this order.
10.Within such time, the Petitioner shall also file a reply to the Show Cause Notice in GST DRC-01 dated 16.08.2024 together with requisite documents to substantiate the case by treating the impugned Order dated 05.02.2025 as an addendum to the Show Cause Notice dated 16.08.2024.
11.In case the Petitioner complies with the above stipulations, the Respondents shall proceed to pass a final order on merits and in accordance with law as expeditiously as possible, preferably, within a period of three (3) months of such reply/pre-deposit. Subject to the Petitioner complying with the above stipulations, the attachment of the bank account of the Petitioner shall also stand automatically vacated.
12. It is made clear that bank attachment shall be lifted subject to the deposit of 10% of the disputed tax as ordered above and no other amount is in arrears barring the amount demanded under the impugned Order.
13. In case the Petitioner fails to comply with any of the stipulations, the Respondents are at liberty to proceed against the Petitioner to recover the tax in accordance with law as if this Writ Petition was dismissed in limine today.
14.Needless to state, before passing any such order, the Respondents shall give due notice to the Petitioner.
15.This Writ Petition stands disposed of with the above observations. No costs. Connected Writ Miscellaneous Petition is closed.
Category: GST

About CA Satbir Singh

Chartered Accountant having 12+ years of Experience in Taxation , Finance and GST related matters and can be reached at Email : Taxheal@gmail.com