Waiver of Late Fee Allowed Even for Returns Filed Before Amnesty Notification

Case Details

• Case Title: Thiruvalla Glass & Plywoods v. Superintendent, Central GST & CE & Union of India

• Court: High Court of Kerala at Ernakulam

• Petition Number: WP(C) No. 42745 of 2024

• Date of Judgment: 31 January 2025

• Category of Dispute: Late Fee under Section 47 of CGST Act – Amnesty Scheme

• Relevant Sections: Section 47 of CGST Act, Notifications No. 7/2023 & 25/2023

Facts of the Case (Paras 2–4)

1. The petitioner, a registered taxpayer, filed its GSTR-9 annual returns belatedly for FY 2018–19 (on 16.03.2023) and FY 2019–20 (on 21.03.2023).

2. A demand notice (Ext. P2) was issued imposing late fee under Section 47 for belated filing of GSTR-1 and GSTR-9 returns.

3. The petitioner claimed benefit of Amnesty Notifications (No. 7/2023 dated 31.03.2023 & No. 25/2023), which waived late fee beyond ₹10,000 for delayed returns filed between 01.04.2023 and 31.08.2023.

4. The department denied the benefit, stating that since the petitioner filed returns before 01.04.2023, it was not eligible under the scheme.

Question in Consideration (Paras 6–7)

• Whether a taxpayer who filed belated returns before the Amnesty Notification period can also claim the benefit of waiver of late fee beyond ₹10,000?

Observations of the Court (Paras 6–9)

1. The court noted that excluding those who filed returns before 01.04.2023, while extending waiver to those filing later, amounts to improper and unjust differential treatment.

2. Citing M/s RT Pharma v. Union of India (2024 HHC 15432), it was held that intention of the Government was to encourage filing of returns, not to punish early filers.

3. Reliance was also placed on Anishia Chandrakanth v. Superintendent (WP(C) 30644/2023), where similar relief was granted.

4. The spirit of the notifications was to waive excessive late fee and promote compliance; thus, those who filed returns before 01.04.2023 also deserve equal benefit.

Judgment of the Court (Paras 9–10)

1. Ext. P2 demand quashed to the extent it imposed late fee of ₹2,65,000 on delayed GSTR-9 returns, except ₹10,000 per year which remains payable.

2. Regarding late fee on GSTR-1 returns, petitioner was directed to pursue statutory remedies.

3. The period spent in pursuing this writ petition (29.11.2022–31.01.2025) was directed to be excluded while computing limitation for appeal.

Between Fine Lines (Simple Summary in 5 points)

• The High Court held that taxpayers who filed belated returns before the Amnesty period must also get the late fee waiver benefit.

• Denying waiver to early filers is unjust and against the intent of the scheme.

• Excess late fee demand beyond ₹10,000 per year for GSTR-9 was set aside.

• On GSTR-1 late fee, the petitioner must use normal appeal remedies.

• The ruling ensures fairness and equal treatment for all taxpayers, regardless of timing of filing.

Summary of Referred Cases

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