The Madras High Court ruled that late fees under Section 47 are applicable for delays in filing GSTR-9C, as it is considered part of the annual return under Section 44. In the case of Tvl. Madhu Agencies, the company filed its GSTR-9 for the 2021–22 assessment year with a 13-day delay and paid the late fee. However, its GSTR-9C, required due to a turnover exceeding ₹5 crore, was filed much later in 2025, reportedly due to technical issues. The tax department deemed the return incomplete without the GSTR-9C and imposed a late fee of ₹1,69,400 under Section 47.
The petitioner challenged this, arguing that the late fee should only apply to GSTR-9, not GSTR-9C, and sought amnesty or waiver benefits. However, the court found that Section 44 indicates the annual return includes a reconciliation statement, and Rule 80(3) mandates GSTR-9C for certain taxpayers. Thus, filing GSTR-9 alone does not satisfy compliance requirements, and the term "includes" in Section 44 expands the return's scope to incorporate GSTR-9C where applicable.
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The court emphasized that Section 47 imposes late fees for failure to furnish returns under Section 44. Since GSTR-9C completes the return, delays in its filing attract late fees. The court rejected reliance on contrary High Court rulings and ruled that waiver benefits were unavailable as the petitioner missed the prescribed amnesty timeline for GSTR-9C.
Order Date - 16 April 2026
Parties: Tvl. Madhu Agencies Vs State Tax Officer, Woraiyur Assessment Circle
Facts -
- Tvl. Madhu Agencies, a GST-registered entity, filed its annual return (GSTR-9) for AY 2021–22 with a delay of 13 days and paid the applicable late fee.
- Since its turnover exceeded ₹5 crore, it was also required to file GSTR-9C, but this was filed much later (in 2025), allegedly due to technical glitches.
- The department treated the return as incomplete without GSTR-9C and imposed a late fee of ₹1,69,400 under Section 47.
- The petitioner challenged this, arguing that late fee applies only to GSTR-9 and not to GSTR-9C, and also sought benefit of amnesty/waiver notifications.
Issue -
Order -
- The Court analysed Section 44 and held that the annual return may include a reconciliation statement, and Rule 80(3) makes GSTR-9C mandatory for specified taxpayers. Thus, filing GSTR-9 alone is not sufficient compliance.
- It clarified that the term “includes” in Section 44 expands the scope of the return, meaning GSTR-9C becomes an integral part of the return where applicable. Hence, non-filing of GSTR-9C amounts to non-filing of return itself.
- The Court emphasized that Section 47 imposes late fee for failure to furnish returns under Section 44, and since GSTR-9C completes the return, delay in filing it attracts late fee. Penal provisions must be strictly interpreted but cannot be artificially restricted.
- It rejected reliance on contrary High Court rulings and held that waiver benefits were unavailable since the petitioner failed to file GSTR-9C within the prescribed amnesty timeline.
