Facts of the Case:

In this case, the petitioner for the Financial Year 2021–22, filed the annual return in Form GSTR-9 with a delay of 13 days and duly paid the applicable late fee. Since the petitioner’s turnover exceeded ₹5 crore, it was also required to furnish a reconciliation statement in Form GSTR-9C in terms of Section 44 read with Rule 80(3) of the CGST/TNGST Rules. However, the petitioner filed Form GSTR-9C belatedly, much after filing GSTR-9. The Department treated the filing of GSTR-9C as an essential component of the annual return and computed the delay up to the date of filing of GSTR-9C, thereby levying additional late fee under Section 47. 

Aggrieved by such levy, the petitioner filed a writ petition challenging the assessment order, contending that late fee is applicable only for delay in filing GSTR-9 and not for delay in filing GSTR-9C.

Issue:

Whether late fee under Section 47 of the CGST/TNGST Act, 2017 can be levied for delay in filing Form GSTR-9C (reconciliation statement), treating it as part of the annual return under Section 44?

Held That:

The Court held that Form GSTR-9C is an integral and mandatory part of the annual return under Section 44, particularly for taxpayers whose turnover exceeds ₹5 crore. It was observed that the expression “may include” used in Section 44 expands the scope of the annual return to encompass the reconciliation statement, and Rule 80(3) makes its filing compulsory by using the expression “shall furnish… along with the annual return.” Consequently, filing GSTR-9 without GSTR-9C amounts to incomplete compliance and is equivalent to non-filing of the return under Section 44.

The Court further held that since Section 47(2) imposes late fee for failure to furnish the return within the prescribed time, the delay in filing GSTR-9C attracts such levy. The contention that GSTR-9C arises only from the Rules and not from the Act was rejected, as the Rule operates within the statutory framework of Section 44. The Court also denied the benefit of amnesty due to non-compliance within the prescribed timeline and declined to follow the contrary view taken in Anishia Chandrakanth vs Superintendent Central Tax.

Accordingly, the writ petition was dismissed, and the levy of late fee for delayed filing of Form GSTR-9C was upheld.

Case Name: Tvl. Madhu Agencies, Represented by its Proprietrix G. Valliammai Versus The State Tax Officer, Trichy. dated 16.04.2026