The Central Board of Indirect Taxes and Customs (CBIC) has issued a crucial clarification regarding the levy of late fees for delays in furnishing the reconciliation statement in FORM GSTR-9C under the Goods and Services Tax (GST) framework.
This clarification comes in the wake of several representations requesting clarity on whether late fees would apply when the GSTR-9C is filed after the due date, even if it is filed beyond the deadline for submitting the annual return in FORM GSTR-9.
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The clarification addresses the question of whether a late fee, under Section 47 of the Central Goods and Services Tax (CGST) Act, will be applicable if the GSTR-9C is filed after the due date.
The CBIC clarified that a registered taxpayer is required to file the annual return (GSTR-9) along with a reconciliation statement (GSTR-9C) if their aggregate turnover exceeds the prescribed threshold, which currently stands at ₹5 crore.
Under the GST provisions, a complete annual return includes both the GSTR-9 and the self-certified reconciliation statement in GSTR-9C. If the reconciliation statement is not filed along with the GSTR-9, the filing of the annual return is considered incomplete, and the taxpayer will be liable to a late fee.
According to Section 47(2) of the CGST Act, a late fee is applicable for the delay in furnishing the complete annual return, which includes both FORM GSTR-9 and FORM GSTR-9C. However, the CBIC clarified that the late fee would not be calculated separately for the delayed submission of GSTR-9 or GSTR-9C but rather for the entire delayed filing of the annual return.
In cases where the reconciliation statement is not required, the late fee applies only to the delay in submitting GSTR-9. For taxpayers who were supposed to file both forms, the late fee will be applicable from the due date for submitting the complete annual return (both GSTR-9 and GSTR-9C) until the actual date of filing.
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In a significant relief to taxpayers, the CBIC also highlighted that through Notification No. 08/2025-Central Tax, the late fee for delayed filing of the complete annual return for any financial year up to FY 2022-23 has been waived. This waiver applies as long as the GSTR-9C is filed by March 31, 2025.
The waiver covers the late fee exceeding the amount payable under Section 47, as long as the GSTR-9C is furnished before the specified deadline. However, no refund will be issued for late fees already paid, as per the circular.
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