Madras HC Holds Annual Return Not Complete Without GSTR-9C; Sustains Late Fee on Delay

The Madras High Court, in a recent significant ruling, has clarified that GSTR-9C is part of the annual return under the GST law. Non-filing makes the GSTR-9 incomplete; in such a case, a late fee under Section 47 applies.

In the present case, a late fee, totally amounting to Rs 1.69 lakh (Rs 84,700 for SGST and Rs 84,700 for CGST), was imposed on the petitioner, Tvl. Madhu Agencies, for the late furnishing of the reconciliation statement in Form 9-C for the financial year 2021-22. The legal due date for filing the annual return in Form GSTR-9 was December 31, 2022; however, the petitioner furnished the form on January 13, 2023, which caused an explicit delay of 13 days.

Since the total turnover of the petitioner was over the threshold of Rs 5 lakh, it was required to furnish Form GSTR-9C along with the annual return. However, the petitioner failed at the same time and lately furnished Form GSTR-9C on May 09, 2025. In conclusion, the tax authorities levied the late fee by treating the date of filing of Form GSTR-9C as the date of proper filing of the annual return in Form GSTR-9.

The petitioner argued that, as per the provisions of Section 47 of the TNGST Act, 2017, the late fee is only applicable in cases where the annual return is filed late in Form GSTR-9, not for GSTR-9C. Further claimed that the reconciliation statement requirement comes from rules, not directly from the act, and therefore should not attract penalties.

The assessee claimed, “Under Section 47 of the TNGST Act, 2017, the late fee is only applicable for delays in filing the annual return in Form -9. Since the return was filed 13 days late, for which the late fee has already been paid, it cannot be extended to cover the delay in filing the reconciliation statement. Therefore, the impugned order is unsustainable.”

However, the Court rejected the arguments. It explained that under Section 44 of the GST Act, the annual return can include a reconciliation statement, and Rule 80(3) makes it mandatory for businesses with turnover above Rs 5 crore to file GSTR-9C along with GSTR-9. The Court emphasised that filing GSTR-9 without GSTR-9C is considered an incomplete filing of returns.

The Court also clarified that the term “includes” in the law expands the ambit, meaning GSTR-9C becomes part of the annual return. Therefore, not filing it with the legal deadline is considered a failure to file the required return, attracting late fees under Section 47. Since the petitioner did not file GSTR-9C within the statutory deadline, allowed as per the law, the late fee was held valid. With the aforementioned directions, the writ petition has been dismissed, but the petitioner is allowed to file an appeal on factual grounds.