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Article Dated 20th January, 2026

By Tejus R. Pandya, Navsari

Applicability of Penalty under Section 125 for Late Filing of GSTR-3B (With reference to Palani Ilantirayan vs Deputy Commissioner)

1. Issue Involved

Whether penalty under Section 125 of the CGST Act, 2017 can be imposed for late filing of GSTR-3B when a specific late fee is prescribed under Section 47 of the Act.

2. Statutory Provisions

Section 47 – Late Fee for Delay in Filing Returns Section 47 of the CGST Act provides a specific mechanism for levy of late fee for delay in filing returns including GSTR-3B. The late fee is prescribed on a per day basis subject to a maximum limit, as notified.

Section 125 – General Penalty Section 125 is a residuary provision which provides for penalty only in cases where no separate penalty is provided elsewhere in the Act for a particular contravention.

3. Legal Principle

It is a settled principle of law that where a specific provision exists, a general provision cannot be invoked. Section 47 being a specific provision governing delay in filing returns, penalty under Section 125 cannot ordinarily be imposed for the same default. Levy of both would amount to double punishment for the same offence.

4. Judicial Position – Palani Ilantirayan vs Deputy Commissioner (ST) Madras High Court, W.P. No. 23513 of 2021, Order dated 02.09.2021

Facts of the Case:

• The petitioner had failed to file GST returns for a prolonged period

• Repeated opportunities were provided by the department

• There was continuous and persistent non-compliance

Findings of the Court:

• Filing of returns is a statutory obligation

• Continuous non-filing disrupts the GST mechanism

• In cases of persistent default, penalty under Section 125 can be invoked

5. Scope and Limitation of the Judgment

The judgment does not lay down that penalty under Section 125 is automatically leviable for every delay in filing GSTR-3B. The Court did not examine or decide whether Section 125 can be imposed in addition to late fee under Section 47 for mere belated filing.

The case relates to habitual and prolonged non-filing, not routine or technical delay.

6. Distinction Between Late Filing and Non-Filing

Mere delay in filing return:

• Covered specifically under Section 47

• Only late fee is leviable

Persistent or willful non-filing:

• May attract Section 125 based on facts

• Depends on gravity and duration of default

7. Current Legal Position

• Late filing of GSTR-3B attracts only late fee under Section 47

Section 125 cannot be invoked when a specific late fee provision exists

• Palani Ilantirayan judgment is applicable only in cases of continuous and willful noncompliance

• Routine invocation of Section 125 for delayed filing is legally unsustainable

8. Conclusion

Penalty under Section 125 of the CGST Act is not applicable for late filing of GSTR-3B when late fee under Section 47 has already been prescribed and levied. The reliance on Palani Ilantirayan vs Deputy Commissioner for imposing penalty in cases of mere delay is misplaced and contrary to settled principles of statutory interpretation.

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