Late Fees Apply Equally To Non-Filing Of GST Annual Returns And General Penalty Can Be Levied In Addition To Late Fees As No Separate Penalty Exists

By | June 13, 2026

Late Fees Apply Equally To Non-Filing Of GST Annual Returns And General Penalty Can Be Levied In Addition To Late Fees As No Separate Penalty Exists

Issue

  1. Whether a statutory late fee under Section 47 of the CGST/TNGST Act, 2017 can be levied for the absolute non-filing of an annual return (Form GSTR-9), or if it applies strictly to instances of belated/delayed filing.

  2. Whether the revenue department is legally justified in imposing a general penalty under Section 125 in addition to a late fee under Section 47 for the same default of failing to furnish an annual return.

Facts

  • The Default: For the financial period 2017-2018, the petitioner failed to furnish the mandatory annual return in Form GSTR-9 within the prescribed statutory due date.

  • Administrative Action: The tax authority passed an order imposing both a statutory late fee and an additional general penalty on the petitioner for this default.

  • Petitioner’s First Contention: The petitioner filed a writ petition arguing that a “late fee” is conceptually and textually intended to penalize a delayed submission (“belated filing”) and cannot be legally triggered in cases where no return has been filed at all (“non-filing”).

  • Petitioner’s Second Contention: The petitioner further argued that imposing a general penalty alongside a late fee for the exact same non-compliance amounts to double jeopardy or duplicative punishment for a single infraction.

Decision

  • Held, In Favor of Revenue (Issue I): The levy of the late fee is entirely valid, and the petitioner’s argument distinguishing non-filing from belated filing is untenable. The plain text of Section 47 mandates that a late fee is attracted the moment a registered person “fails to furnish” the return by the due date. The statutory late fee of ₹100 per day of default (subject to a maximum cap of 0.25% of the total turnover) applies continuously from the day after the due date, regardless of whether the return is eventually filed late or not filed at all.

  • Held, In Favor of Revenue (Issue II): The imposition of the general penalty under Section 125 is sustained. Section 125 acts as a residual clause that enables a penalty up to ₹25,000 for any contravention of the Act or rules where no separate, specific penalty is explicitly provided. Since the GST statute contains no specialized penalty provision tailored for GSTR-9 defaults, the invocation of the general penalty in addition to the automated late fee is structurally and legally justified.

Key Takeaways

  • Non-Filing Does Not Evade Late Fees: A taxpayer cannot escape the accumulation of statutory late fees by simply choosing to never file a return. The infraction commences automatically on the midnight of the due date, and the liability stays locked at the statutory cap even under total non-filing.

  • Distinct Legal Character of Fees vs. Penalties: A late fee under Section 47 is a compensatory, time-bound financial consequence for a scheduling delay, whereas a general penalty under Section 125 is a punitive measure for a statutory breach. They are concurrent liabilities and do not constitute double taxation.

  • Invocation of Residual Penalty Clauses: Taxpayers must recognize that the absence of a specific penalty section for a particular compliance form does not grant immunity; instead, it automatically triggers the application of the omnibus general penalty provision under Section 125.

HIGH COURT OF MADRAS
Tvl. KPK fuel services
v.
State Tax Officer
SENTHIL KUMAR RAMAMOORTHY, J.
WP No. 17421 of 2026
WMP Nos. 18680 & 18682 of 2026
JUNE  2, 2026
Raghunandan Sriram for the Petitioner. Ms. Amirta Poonkodi Dinakaran, Govt. Counsel (Tax) for the Respondent.
ORDER
1. An order dated 13.12.2023 imposing a late fee and penalty on the petitioner for failure to file the annual return in Form GSTR-9 is the subject of the challenge in this writ petition.
2. Ms. Amirta Poonkodi Dinakaran, learned Government Counsel (Tax), accepts notice on behalf of the respondent.
3. Learned counsel for the petitioner contends that the time limit for filing an annual return for a financial year is three years from the due date of furnishing said annual return. As regards the Assessment Year 2017-2018, he submits that a notification was issued fixing the due date of 05.02.2026. Reckoning the three-year period therefrom, he submits that the three year period lapsed in February 2023. Adverting to the impugned order, learned counsel contends that it erroneously records that the taxpayer filed the return on 07.12.2022. He adds that a late fee may be levied only in respect of belated filing of a return, but not in respect of non-filing thereof.
4. Sub-Section (2) of Section 47 of the Central Goods and Service Tax (CGST) Act, 2017, governs the issue. The said provision is set out below:
“Section 47 Levy of Late Fee.
(1) …………………………….
(2) Any registered person who fails to furnish the return required under Section 44 by the due date shall be liable to pay a late fee of one hundred rupees for every day during which such failure continues subject to a maximum of an amount calculated at a quarter per cent. Of his turnover in the State or Union Territory.”
5. From the text of Sub-Section (2), it is evident that late fees is leviable on a registered person who fails to file the return by the due date. The said late fee is leviable at Rs.100 per day of default, subject to the maximum of not more than 0.25% of the turnover.
6. Learned counsel for the petitioner also contends that the penalty under Section 125 of applicable GST enactments cannot be imposed after levying a late fee. Section 125 enables the imposition of penalty of up to Rs.25,000/- for contravention of any provisions of the applicable GST statutes or rules framed thereunder, provided no separate penalty is prescribed under the statute in respect thereof. On perusal of applicable statutes, no separate penalty is prescribed in respect of failure to file the annual return. Hence, the imposition of penalty is in order.
7. Thus, the contention of learned counsel for the petitioner is untenable and Section 47(2) enables the levy of late fee, if a taxpayer fails to file the return. In view thereof, there is no infirmity in the impugned order warranting interference under Article 226 of the Constitution of India.
8. For the reasons aforesaid, this Writ Petition stands dismissed. No costs. Consequently, the connected Miscellaneous Petitions are closed.