GST Amnesty for Late Fee Waiver on GSTR-9 & 9C Applies to Returns Filed Before Notification: Himachal Pradesh HC [Read Order]

The Himachal Pradesh High Court has ruled that taxpayers who filed their ( Goods and Services Tax Returns ) GSTR-9 and GSTR-9C returns before the amnesty notification date can still avail of the late fee waiver benefit.

The bench of Acting Chief Justice Tarlok Singh Chauhan and Justice Satyen Vaidya observed that the government's intention behind the notification was not to penalize taxpayers but to encourage the filing of returns for the specified assessment years. Considering this, the court held that the benefit of the amnesty scheme should extend to the petitioner, who had filed the return belatedly on 13.03.2023—before the cut-off date mentioned in the notification.

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In the petition filed by a pharmaceutical company named R T Pharma, a registered company under GST, which faced financial distress and filed its returns belatedly on March 13, 2023, well before the government’s amnesty notification dated March 31, 2023 (Notification No. 07/2023).

The petitioner was served a show cause notice on August 22, 2023, imposing a late fee of ₹12,71,754, as the authorities argued that the amnesty scheme was only applicable to returns filed between April 1, 2023, and June 30, 2023. The petitioner contended that the amnesty’s objective was to encourage tax compliance and should extend to those who voluntarily filed returns before the notification date.

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The petitioner relied on a similar judgment by the Kerala High Court in Anishia Chandrakanth v. Superintendent, Central Tax and Central Excise, where it was observed that “When the Government itself has waived late fee under the aforesaid tow notifications Nos. 7/2003 dated 31.03.2023 and 25/2023 dated 07.07.2023 in excess of Rs. 10,000/-, in case of non-fliers there appears to be no justification in continuing with the notices for non payment of late fee for belated GSTR 9C, that too filed by the taxpayers before 01.04.2023, the date on which one time amnesty commences.”

In the above decision, the Kerala high court found it unjust and unsustainable to the extent it sought to collect late fee for delay in filing GSTR 9C. However, it is made clear that the petitioners will not be entitled to claim refund of the late fee which has already been paid by them over and above Rs. 10,000/-.

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The respondents argued that the amnesty scheme under Notification No. 7/2023, dated 31.03.2023, was only applicable to taxpayers who failed to file their returns within the stipulated amnesty period.

They contended that, in this case, the deadline for filing the return had expired on 07.02.2020, while the petitioner submitted the return on 13.03.2023—before the amnesty period (01.04.2023 to 30.06.2023) began. Therefore, they claimed that the petitioner was not eligible for the benefits of the notification.

The court noted that it would be unjust to deny the petitioner the benefit solely because the return was filed before the issuance of the amnesty notification on 31.03.2023, which provided relief only to those filing between 01.04.2023 and 30.06.2023.

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Recognizing the broader intent of the notification, the court ruled in favor of the petitioner. Consequently, it set aside the impugned order dated 30.11.2023 and the show-cause notice dated 22.08.2023 issued under Section 74 of the Act.

The matter was remanded to the third respondent, directing them to pass a fresh order on merit while extending the benefit of the notification in accordance with the law. The court also directed that the revised order be issued expeditiously, preferably within three months from the receipt of the judgment.

To Read the full text of the Order CLICK HERE

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