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AURIGA ACCOUNTING PRIVATE LIMITED Himachal Pradesh HC Late Fee Waiver for Pre Amnesty GSTR 99C Filings

The Himachal Pradesh High Court has held that taxpayers who filed their GST annual returns (GSTR-9 and GSTR-9C) before the issuance of the amnesty notification are still entitled to a waiver of late fees. While the notification specified that the waiver applies only to returns filed within a specific timeframe, the court emphasized that the core objective of the amnesty scheme is to encourage tax compliance—not to penalize those who filed before the scheme was announced. This ruling offers significant relief to taxpayers who were previously excluded from the waiver despite timely compliance.

Key Highlights from Himachal Pradesh High Court’s Ruling on GST Amnesty Scheme

1. Extension of Amnesty Scheme Eligibility
The Himachal Pradesh High Court has ruled that taxpayers who filed their GSTR-9 and GSTR-9C returns before the issuance of Notification No. 07/2023 are also eligible for a waiver of late fees.

2. Purpose of the Amnesty Scheme
The court emphasized that the amnesty scheme’s intent is to promote tax compliance, not to penalize taxpayers for late filings, especially those who took the initiative to comply voluntarily.

3. Court’s Decision
The court set aside the late fee demand of ₹12,71,754 and directed the tax authorities to issue a fresh order granting the benefit of the amnesty scheme to the petitioner.

4. Relief for Taxpayers
This decision brings significant relief to businesses and individuals who filed returns prior to the amnesty notification but were denied the waiver. It also underscores the importance of equitable implementation of such schemes.

5. Legal Safeguard for Taxpayers
The ruling reinforces the judiciary’s role in ensuring that government policies support voluntary compliance and prevent arbitrary penalization of taxpayers

Background of the Case

A pharmaceutical company registered under GST had filed its GSTR-9 and GSTR-9C returns on March 13, 2023, due to financial distress. The GST amnesty notification (No. 07/2023) was later issued on March 31, 2023, covering returns filed between April 1 and June 30, 2023.

Despite its timely filing before the notification, the company received a show-cause notice on August 22, 2023, demanding a late fee of ₹12,71,754. The authorities contended that the company was ineligible for relief as its filing fell outside the prescribed window.

The company argued that the objective of the amnesty scheme was to encourage compliance, and taxpayers who filed voluntarily before the notification date should not be excluded.

Court’s Final Observations on GSTR-9 & 9C Late Fee Waiver

The High Court sided with the taxpayer, stating that it would be unjust to deny relief merely based on the filing date when the taxpayer had already complied voluntarily. The ruling recognized that the scheme was intended to ease the compliance burden, not to punish those who had acted in good faith. Accordingly, the late fee demand was quashed.

What This Means for Taxpayers

This ruling is a milestone judgment for taxpayers in similar circumstances. It provides strong legal precedent for challenging late fee demands if returns were filed before the amnesty notification but relief was denied.

Are You Eligible for the GST Amnesty Scheme?

If you’re unsure whether you qualify for benefits under the GST Amnesty Scheme, it’s crucial to assess your filing history. For assistance in filing GSTR-9 or GSTR-9C or claiming relief under the amnesty provisions, the experts at Auriga Accounting pvt. ltd. are here to help.

Get in touch today to ensure full compliance and avoid unnecessary penalties

About the Author

Manisha

Manisha is a seasoned content writer with expertise in business registration, tax laws, trademark regulations, and corporate compliance. His well-researched articles offer practical, easy-to-understand guidance, empowering businesses to navigate complex legal and regulatory landscapes with confidence

January 8, 2026

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