GSTR-9C Mandatory – Late Fee Continues Till Filing | HC

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GSTR-9C late fee
Case Details: Tvl. Madhu Agencies vs. State Tax Officer (2026) 41 Centax 266 (Mad.)

Judiciary and Counsel Details

  • D. Bharatha Chakravarthy, J.
  • Shri N.Sudalai Muthu, for the Petitioner.
  • Shri R.Suresh Kumar, Additional Government Pleader, for the Respondent.

Facts of the Case

The petitioner, being a registered person with turnover above Rs. 5 crores, filed GSTR-9 with delay and paid late fee. The petitioner failed to furnish GSTR-9C along with the annual return and filed it later. The assessment order treated the date of filing of GSTR-9C as the date of proper filing of the annual return. Late fee was levied for belated filing of the reconciliation statement. It was contended that late fee under section 47 was applicable only for delay in filing GSTR-9 and not for delay in filing GSTR-9C. It was further contended that the requirement to file reconciliation statement was not mandatory under section 44. It was also contended that the amnesty granted for filing the annual return should be taken into account and a higher penalty need not be levied for Form GSTR 9C. The matter was accordingly placed before the High Court.

High Court Held

The High Court held that the expression ‘may include a self-certified reconciliation statement’ enlarged the scope of the annual return. It was held that Rule 80(3) mandated the furnishing of GSTR-9C along with the annual return. It was further held that filing of GSTR-9 without GSTR-9C amounted to non-filing of return under section 44 and attracted a late fee under section 47. It was observed that GSTR-9C completed the annual return and justified the levy of the late fee till its filing. It was also held that a waiver under Notification No. 08/2025–Central Tax, dated 23-01-2025, read with Circular No. 246/03/2025-GST, dated 30-10-2025, was available only where GSTR-9C was filed on or before 31-03-2025. It was observed that filing beyond such a date rendered the waiver unavailable. Accordingly, the writ petition was dismissed with liberty to prefer an appeal.

List of Cases Cited

  • Anishia Chandrakanth v. Superintendent, Central Tax & Central Excise — [2024] 162 taxmann.com 115 (Kerala) = [2024] 104 GST 512 (Kerala) = 2024 (86) G.S.T.L. 266 (Kerala) — Referred [Para 21]
  • CIT v. Ramco Cements Ltd. — T.C.A. No. 966 of 2013, dated 4-4-2022 — Referred [Para 20]
  • Commissioner of Customs v. Caryaire Equipment India Pvt. Ltd. — (2012) 4 SCC 645 — Referred [Para 18]

List of Departmental Clarification Cited

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