Missed Filing GSTR-9 or GSTR-9C? Here's How You Can Still Comply without Additional Penalties

The Central Board of Indirect Taxes and Customs (CBIC) has issued Notification No. 08/2025, offering relief to taxpayers who missed filing GSTR-9 or GSTR-9C for the financial years 2017-18 to 2022-23.

This notification allows taxpayers to file their pending returns without incurring additional late fees, provided they do so before March 31, 2025. Any late fees already paid will not be refunded. With the deadline fast approaching, taxpayers must take immediate action to avoid penalties and potential scrutiny from the GST department.

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Understanding GSTR-9 and GSTR-9C

Before diving into the details of the waiver, let’s clarify the purpose of these two forms:

GSTR-9 (Annual GST Return)

• It is a consolidated return that registered taxpayers (excluding certain categories like Input Service Distributors and non-resident taxpayers) must file annually.
• Who Needs to File? Taxpayers with an aggregate turnover exceeding Rs. 2 crore in a financial year.
• Deadline: December 31 of the following financial year.

GSTR-9C (Reconciliation Statement)

• This is a self-certified reconciliation statement that aligns the taxpayer’s GSTR-9 return with their audited financial statements.
• Who Needs to File? Businesses with a turnover of more than Rs. 5 crore.
• Certification: It must be certified by a Chartered Accountant (CA) or another qualified professional.

Failure to file these returns on time can lead to penalties, additional scrutiny, and even audits by the GST authorities.

Highlights of Notification No. 08/2025

The latest notification provides relief by waiving the excess late fee for delayed GSTR-9C filings under certain conditions:

• Waiver Scope: The waiver applies to taxpayers who failed to file GSTR-9C on time but have now decided to comply before March 31, 2025.
• Late Fee Already Paid? No refunds will be granted for previously paid late fees.
• Show Cause Notices (SCNs): If a taxpayer has received an SCN for late filing of GSTR-9C, they can request cancellation of the notice by completing the filing before the deadline.

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Conditions for Late Fee Waiver

To benefit from this waiver, taxpayers must meet one of the following conditions:

1. GSTR-9 was Filed on Time: If GSTR-9 was submitted on time, then GSTR-9C can be filed without additional penalties.
2. GSTR-9 was Filed Late, but Late Fees Were Paid: If late fees for GSTR-9 have already been paid, additional fees for GSTR-9C will not be imposed.
3. Taxpayer Received a Show Cause Notice (SCN): Taxpayers who received SCNs for non-filing of GSTR-9C can now file the return to cancel the notice and avoid further legal consequences.

Late Fees on GSTR-9 and GSTR-9C

As per Section 47 of the CGST Act, 2017, the following late fees are applicable:

Turnover in Financial Year	Per Day Late Fee	Maximum Late Fee
Up to Rs. 2 Crore	No Late Fee	Not Applicable
Rs. 2 Crore – Rs. 5 Crore	Rs. 50	0.04% of turnover in the State/UT
Rs. 5 Crore – Rs. 20 Crore	Rs. 100	0.04% of turnover in the State/UT
Above Rs. 20 Crore	Rs. 200	0.50% of turnover in the State/UT

As per Notification 14/2024, taxpayers with turnover up to Rs. 2 crore are exempted from filing GSTR-9 for FY 2023-24. Notification 7/2023 introduced late fees for turnover categories starting from FY 2022-23. Section 47(2) of the CGST Act, 2017 applies for businesses with turnover above Rs. 20 crore.

Why Timely Filing is Crucial

The waiver offers relief but the taxpayers must take action before March 31, 2025, to avoid complications. Failing to file GSTR-9C before the deadline can result in:

• Monetary Penalties: Under Section 125 of the CGST Act, a penalty of up to Rs. 25,000 may be imposed for non-compliance.
• Increased GST Scrutiny: Non-filers may be subject to detailed audits and compliance checks by the GST department.
• Risk of Tax Audits: The GST department may conduct audits or investigations to detect tax evasion or discrepancies in filings.

Looking for a Detailed, Line-by-Line Breakdown of Every Section in the CGST Act? Click Here

Conclusion

The CBIC’s waiver of late fees for GSTR-9C filings presents a valuable opportunity for businesses to rectify past non-compliance without incurring excessive penalties. The waiver only applies to GSTR-9C, not GSTR-9.

With the March 31, 2025 deadline in place, taxpayers must act quickly to ensure compliance, avoid legal repercussions, and maintain a smooth tax record. Ignoring this deadline may lead to severe consequences, including penalties, increased scrutiny, and potential audits.

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