Whether late fee under section 47 of the CGST Act, 2017 can be demanded for delayed filing of GSTR-9 / GSTR-9C where the Government itself has granted amnesty and partial waiver of late fee under Notifications No. 7/2023-CT and 25/2023-CT, and whether general penalty under section 125 can be imposed in addition to late fee.
The court treated continuation of higher late-fee demands post-amnesty as a question of legality, not administrative discretion.
2. Sections and Rules Discussed
Section 44, CGST Act, 2017
Section 47, CGST Act, 2017 (Late Fee)
Section 125, CGST Act, 2017 (General Penalty)
Section 128, CGST Act, 2017 (Power to waive penalty / late fee)
Multiple writ petitions were filed by registered persons challenging:
Levy of excessive late fee for delayed filing of Annual Returns (GSTR-9 / GSTR-9C) for FYs 2017-18 to 2021-22; and
Simultaneous imposition of general penalty under section 125 in addition to late fee under section 47.
During the pendency of disputes, the GST Council in its 49th meeting recommended rationalisation of late fee and introduction of a one-time amnesty. Pursuant thereto, Notifications No. 07/2023-CT and 25/2023-CT were issued, capping late fee at ₹10,000 and granting waiver of late fee in excess thereof.
Despite this, notices and demands continued to be issued in several cases, even where returns were filed before the amnesty window.
The dispute turned primarily on timing of filing vis-à-vis the amnesty notifications rather than the fact of delay itself
4. Appellant’s Submissions
Once the Government has exercised power under section 128 and waived late fee beyond ₹10,000, continuation of proceedings for higher late fee is arbitrary and unjustified.
Late fee under section 47 is penal in nature; therefore, general penalty under section 125 cannot be imposed simultaneously.
Denying the benefit of amnesty to persons who filed returns before 01.04.2023 amounts to hostile discrimination, violative of Article 14.
Reliance was placed on decisions of Kerala High Court and Himachal Pradesh High Court granting similar relief.
Readers can note that the assessees successfully framed the issue as one of constitutional equality, not mere statutory concession.
5. Department’s / Respondent’s Submissions
Notifications granting amnesty are prospective and applicable only to non-filers who availed the specified window.
Taxpayers who filed returns prior to the notification date cannot automatically claim its benefit.
Late fee is statutorily leviable under section 47, and the department was justified in issuing notices for recovery.
6. Analysis and Findings of the Court
The Court undertook a detailed analysis of:
The nature of late fee under section 47, holding it to be penal in substance, though not expressly termed as “penalty”;
The object and intent behind Notifications No. 07/2023-CT and 25/2023-CT, issued pursuant to GST Council recommendations.
Key findings:
Once late fee is levied under section 47, there is no scope for simultaneous imposition of general penalty under section 125.
The benefit of concessional late fee cannot be denied to taxpayers who filed annual returns before the cut-off date, as doing so would result in arbitrary and discriminatory treatment.
Continuation of notices demanding late fee in excess of ₹10,000, despite amnesty notifications, was held to be unsustainable in law.
However, taxpayers are not entitled to refund of late fee already paid beyond ₹10,000 unless specifically permitted.
7. Final Judgment / Operative Directions
Demands for late fee in excess of ₹10,000 were set aside.
General penalty under section 125 imposed alongside late fee was quashed.
Petitioners were held liable only to the extent of ₹10,000 late fee under section 47.
No refund of excess late fee already paid was directed.
Batch of writ petitions allowed accordingly.
8. Similar / Related Judgments & Counter Judgments
Supporting / Similar Judgments
R.T. Pharma vs. Union of India – Himachal Pradesh High Court
Anishia Chandrakanth vs. Superintendent of Central Tax – Kerala High Court
Tvl. Jainsons Castors and Industrial Products – Madras High Court
Counter / Contrary Judgments
Cases where late fee was upheld due to continued default or filing beyond amnesty window (fact-specific).
9. CA BTA Insights (Professional Takeaway)
This is a landmark ruling on late fee jurisprudence under GST. It firmly establishes that:
Late fee and general penalty cannot coexist;
Amnesty notifications must be applied uniformly and non-discriminatorily;
Section 128 waivers have real legal force, not merely administrative discretion.
For practitioners:
This judgment is highly effective in replying to recovery notices for late fee / penalty.
Strongly usable in rectification applications, appeals, and writ petitions involving GSTR-9 / 9C late fee.
Especially relevant for legacy GST disputes (2017-18 to 2021-22).
This update materially strengthens taxpayer defence on late fee rationalisation and penalty overreach. Copy of the judgement is attached here.