CBIC Announces Major Changes to GST Refund and Appeal Rules

Introduction

The Central Board of Indirect Taxes and Customs (CBIC) has introduced significant amendments to the Goods and Services Tax (GST) framework through Notification No. 23/2025–CT dated 10 May 2025. Issued under the Central Goods and Services Tax (Second Amendment) Rules, 2025, these changes bring substantial updates to GST refund and appeal procedures and will take effect from May 2025.

The reforms hold particular importance for exporters, small and medium enterprises (SMEs), and taxpayers engaged in filing appeals or claiming refunds under the CGST Act. This article provides a detailed overview of the key amendments, examines their potential business implications, and outlines the steps stakeholders should take to ensure compliance under the revised regulatory framework.

Key GST Refund and Appeal Amendments in 2025

The amended CGST Rules introduce several important changes aimed at streamlining GST appeal and refund procedures. Below is a summary of the most significant updates and their implications for businesses.

1. Standardised Timelines for GST Appeal Filing

One of the most notable procedural reforms is the clarification of timelines for filing GST appeals under Rule 108.

Earlier Position
Previously, the rules did not clearly prescribe a mandatory digital filing mechanism or uniform timelines, resulting in ambiguity and varied practices across jurisdictions.

What Has Changed (Effective May 2025)

Appeals must be filed electronically in Form APL-01 within three months from the date of the order.
A one-month extension may be granted on showing sufficient cause.
Filing through the GST portal is now mandatory.

Business Impact
This amendment removes subjectivity and ensures uniformity. Businesses must closely monitor adjudication orders and initiate appeals promptly to avoid losing their right to appeal.

2. Revised Acknowledgement Process for Appeals (Rule 108(3))

The process for acknowledging appeals has been tightened to ensure timely submission of documents.

Earlier Practice
Acknowledgements could be generated even if the certified copy of the order was uploaded later, creating uncertainty about the actual date of filing.

New Procedure

Acknowledgement will be generated only after uploading the certified copy of the order.
If uploaded within 7 days of filing → the appeal date remains the original filing date.
If uploaded after 7 days → the appeal date shifts to the upload date.

Key Takeaway
Timely uploading of documents is now critical. Delays may impact the limitation period and the admissibility of appeals.

3. Clarification on Refund Refiling After Deficiency Memo (Rule 90(3A))

To address recurring delays in refund processing, especially for exporters, a new provision has been introduced.

Earlier Position
Issuance of a deficiency memo resulted in the ARN being treated as withdrawn, forcing taxpayers to file a fresh refund application.

New Provision

Taxpayers can re-file the refund application using the same ARN after rectifying deficiencies.
No need to generate a new ARN.

Why It Matters
This simplifies the refund process, improves cash flow for exporters, and ensures better continuity and audit tracking.

4. Formal Procedure for Withdrawal of Refund Claims (Form RFD-01W)

A structured mechanism has now been introduced to withdraw refund applications.

What’s New

Refund claims can be withdrawn using Form RFD-01W.
Withdrawal is allowed any time before sanction or rejection.

Business Advantage
This helps businesses correct mistakes, revise claims, and avoid unnecessary disputes or multiple refund cycles.

5. No Refund for Payments Made Before May 2025

The amendments clearly restrict refunds relating to payments made prior to the effective date.

Clarification Issued
Refunds of tax, interest, or penalties paid before May 2025 will not be processed under the amended rules.

Rationale
This ensures finality of settled matters and prevents reopening of past transactions.

Compliance Tip
Businesses should limit refund claims to post-amendment payments and resolve older disputes under earlier provisions.

6. Partial Withdrawal of Appeals – Greater Flexibility

Taxpayers now have the flexibility to manage appeals more strategically.

New Facility

Appeals can be withdrawn partially, covering specific tax periods or issues.
Particularly relevant under the GST Amnesty Scheme.

Why This Is Significant
Businesses can resolve minor disputes while continuing litigation on substantive matters, reducing costs and timelines.

7. Automatic Withdrawal of Appeals under the GST Amnesty Scheme

To reduce litigation backlog, the government has automated appeal withdrawals for certain legacy periods.

Applicable Period
Disputes from 1 July 2017 to 31 March 2020.

Impact
If a taxpayer opts for settlement under the Amnesty Scheme, the related appeals will be deemed withdrawn automatically, leading to faster resolution and improved compliance.

8. Invoice-Level Online Refund Filing (Effective January 2025)

A major procedural shift has been introduced in the refund filing mechanism.

What’s Changing

Refund claims must be filed invoice-wise directly in Form RFD-01 on the GST portal.
Offline utilities will be discontinued.

Benefits

Improved data accuracy and validation
Reduced duplication and errors
Stronger digital audit trails

Action Point
Businesses should ensure their accounting systems support invoice-level GST data and train teams handling refund filings.

Compliance Checklist for Businesses

Compliance Area	Action Required
GST Appeals	File Form APL-01 digitally within 3 months
Certified Order Upload	Upload within 7 days to retain original appeal date
Refund Refiling	Use original ARN after deficiency memo
Refund Withdrawal	Use Form RFD-01W before sanction or rejection
Old Period Refunds	Avoid claims for payments made before May 2025
Partial Appeal Withdrawal	Use selectively for specific periods or issues
Invoice-wise Refund Filing	Prepare systems ahead of January 2025

Key Takeaways for Businesses

Standardised Appeal Timelines: GST appeals must be filed electronically in Form APL-01 within three months from the date of the order, with a possible one-month extension. Digital filing through the GST portal is now mandatory.
Certified Copy Mandatory for Acknowledgement: Appeal acknowledgements will be auto-generated only after uploading a certified copy of the order. Timely upload is essential to retain the original filing date.
Refund Refiling After Deficiency Memo: If a deficiency memo is issued, taxpayers can re-file refund applications using the same original ARN, simplifying and accelerating the refund process.
Facility to Withdraw Refund Claims: Refund applications can now be withdrawn using Form RFD-01W at any stage before sanction or rejection, enabling corrections and revisions without procedural hurdles.
Restriction on Pre-Amendment Refunds: Refund claims relating to tax, interest, or penalties paid before May 2025 will not be admissible under the amended rules, ensuring finality of settled matters.
Partial Withdrawal of Appeals: Taxpayers may now withdraw appeals selectively for specific tax periods or issues while continuing litigation on others, offering greater strategic flexibility.
Automatic Appeal Withdrawal under GST Amnesty Scheme: Appeals relating to the period 1 July 2017 to 31 March 2020 will be deemed withdrawn automatically if the taxpayer opts for settlement under the GST Amnesty Scheme.
Invoice-Wise Online Refund Filing: From January 2025, refund claims must be filed invoice-wise in Form RFD-01 directly on the GST portal, improving data accuracy and system validations.

Actionable Steps for Businesses

Track adjudication orders closely and file Form APL-01 within prescribed timelines.
Upload certified copies of orders promptly to avoid delays in appeal acknowledgement.
Use the same ARN when re-filing refund applications after a deficiency memo.
Withdraw incorrect or premature refund claims through Form RFD-01W when required.
Avoid filing refund claims for payments made before May 2025.
Evaluate the option of partial appeal withdrawal to manage disputes efficiently.
Consider opting for the GST Amnesty Scheme for eligible legacy disputes.
Upgrade accounting and ERP systems to support invoice-level refund filing.

Need Help Navigating the New GST Refund and Appeal Rules?

The recent GST amendments introduce critical procedural changes that demand timely action and meticulous compliance. To avoid missed deadlines, refund delays, or procedural errors, expert guidance is essential.

Auriga Accounting pvt. ltd. offers end-to-end support for GST appeals, refund claims, documentation, and strategic dispute resolution under the revised framework. Connect with our GST professionals today and ensure seamless compliance with confidence.

About the Author

Ravi

Ravi simplifies complex legal concepts into practical, actionable insights, helping entrepreneurs meet their compliance requirements and build sustainable, legally sound businesses.