Major GST Refund and Appeal Rules Announced by CBIC 

The Central Board of Indirect Taxes and Customs (CBIC) has unveiled a crucial set of amendments to the Goods and Services Tax (GST) regime through Notification No. 23/2025–CT dated 10.05.2025, introducing substantial changes to the GST refund and appeal procedures. These modifications, enacted under the Central Goods and Services Tax (Second Amendment) Rules, 2025, will come into force starting May 2025. These reforms are particularly relevant for exporters, small and medium enterprises (SMEs), and any taxpayer involved in filing appeals or seeking refunds under the CGST Act.  In this article, we break down the key amendments, explore their business impact, and outline what stakeholders need to do to stay compliant under the revised framework. 

Key GST Refund and Appeal Amendments in 2025

Here are the most important changes notified under the amended CGST Rules:

1. Revised Timelines for GST Appeal Filing

One of the most important procedural changes is the standardisation of GST appeal filing timelines under Rule 108.

Old Framework

Previously, there was no strict mandate on the digital format for filing appeals. The rules did not clarify the filing mechanism, leaving room for ambiguity and inconsistent practices across jurisdictions.

What’s New

With effect from May 2025:

• Taxpayers must now file GST appeals using Form APL-01 within 3 months from the date of the order.
• This period can be extended by one additional month if a valid reason is provided.
• Mandatory digital filing through the GST portal is now in place.

What Businesses Should Do

This change reduces discretion and brings uniformity to the appeal filing process. Businesses must ensure they track adjudication orders closely and initiate the appeal process promptly to avoid lapse of rights.

2. Certified Copy Upload – Acknowledgement Process Overhauled

Another significant change is the modification in how appeal acknowledgements are handled post-filing.

Earlier Process

Earlier, once Form APL-01 was filed, an acknowledgement could be generated even if a certified copy of the order wasn’t uploaded immediately. This sometimes caused confusion regarding the “official” date of filing.

New Process under Rule 108 (3)

• Acknowledgement will now be auto-generated only after uploading a certified copy of the order.
• If uploaded within 7 days of filing → date of appeal = original filing date.
• If uploaded after 7 days → date of appeal = date of document upload.

Key Takeaway for Businesses

This places the onus squarely on taxpayers to upload documentation in a timely manner. Delay in uploading could impact the admissibility of an appeal due to the expiry of the limitation period.

3. Refund Withholding Clarification – Rule 90(3A)

Refunds, especially for exporters and inverted duty structure claims, often face delays due to provisional withholding by tax officers. A new insertion in the rules addresses this problem.

Previous Practice

When a deficiency memo was issued, the ARN (Application Reference Number) was treated as withdrawn, requiring taxpayers to start over and re-file a new application with a new ARN.

Now Introduced – Rule 90(3A)

• If a deficiency memo is issued, taxpayers are now allowed to re-file using the same original ARN.
• No need to generate a fresh ARN or repeat the initial process.

Why It Matters

This amendment makes the refund process more efficient, especially for exporters, who often face procedural hurdles leading to delayed cash flow. The reuse of the same ARN also ensures continuity and easier audit tracking.

4. Formal Mechanism to Withdraw Refund Claims – RFD-01W

Until now, the withdrawal of refund applications was a grey area with no clear procedure, leading to complications in correcting mistakes.

New Withdrawal Form Introduced

Taxpayers can now:

• Withdraw refund claims using Form RFD-01W.
• Withdrawal is permissible at any point before the refund is either sanctioned or rejected.

Business Benefit

This brings relief for businesses that:

• Filed erroneous or premature refund claims.
• Need to revise applications due to new data or rectifications.

This also avoids multiple refund cycles and miscommunication with GST officers.

5. No Refund on Pre-Amendment Payments

CBIC has blocked refund claims related to payments made before the effective date of the 2025 amendments.

What’s Stated

Refunds of any tax, interest, or penalty paid before May 2025 (implementation date of these rules) will not be entertained under the new provisions.

Rationale

The move is intended to preserve the finality of already-settled accounts and prevent the reopening of closed transactions, which could otherwise burden the system with retrospective claims.

Compliance Tip

Businesses should restrict refund claims to post-amendment transactions only. Historical disputes will need to be resolved under older provisions or existing legal channels.

6. Partial Withdrawal of Appeals – Enhanced Flexibility

In many cases, businesses face disputes across multiple tax periods. Earlier, they were forced to pursue or withdraw appeals in entirety.

New Facility Introduced

Taxpayers can now:

• Withdraw appeals for specific tax periods or issues while continuing to litigate others.
• Available particularly in the context of the GST Amnesty Scheme.

Why It’s a Game-Changer

This allows businesses to:

• Settle minor or resolved issues while contesting material issues.
• Reduce litigation costs and timelines.
• Enjoy more strategic control over dispute resolution.

7. Automatic Appeal Withdrawal under GST Amnesty Scheme

As part of the drive to decongest tribunals and courts, the government has automated appeal withdrawals for certain historical tax periods.

Applicable Period

Disputes pertaining to July 1, 2017, to March 31, 2020.

If the taxpayer opts for settlement under the Amnesty Scheme, then:

• Appeals for the covered periods will be deemed withdrawn automatically.
• Expected Outcome
• Lowers the administrative burden on the appellate system.
• Faster settlement of legacy disputes.
• Encourages voluntary compliance.

8. Invoice-Based Online Refund Filing System (from Jan 2025)

Another major reform on the procedural side is the introduction of an invoice-level refund filing mechanism, effective January 2025.

What’s Changing

• Refund claims will be filed invoice-wise directly into Form RFD-01 on the GST Portal.
• Offline utilities will be phased out.

Key Benefits

• Better data accuracy and system validations.
• Reduces the risk of duplicate claims or errors.
• Strengthens digital audit trails for GST officers and businesses alike.

Actionable Tip

Businesses should:

• Ensure their ERP or accounting systems are integrated with invoice-level GST data.
• Conduct training for staff responsible for GST refunds.

Compliance Checklist for Businesses

Key Takeaways for Businesses

Standardized Appeal Timelines: GST appeals must now be filed using Form APL-01 within 3 months from the date of the order, with a possible 1-month extension. Mandatory digital filing through the GST portal is required.

• Certified Copy Upload for Acknowledgement: Acknowledgement of appeal will be auto-generated only after uploading a certified copy of the order. Timely uploading is crucial to preserve the original filing date.
• Refund Refiling After Deficiency Memo: Taxpayers can now re-file refund applications using the same original ARN if a deficiency memo is issued, streamlining the refund process.
• Withdrawal of Refund Claims: Businesses can withdraw refund claims using Form RFD-01W at any point before the refund is either sanctioned or rejected, allowing for corrections or revisions.
• No Refund on Pre-Amendment Payments: Refunds of any tax, interest, or penalty paid before May 2025 will not be entertained under the new provisions, preserving the finality of already-settled accounts.
• Partial Withdrawal of Appeals: Taxpayers can now withdraw appeals for specific tax periods or issues while continuing to litigate others, offering more flexibility in dispute resolution.
• Automatic Appeal Withdrawal under GST Amnesty Scheme: Appeals for the period from July 1, 2017, to March 31, 2020, will be deemed withdrawn automatically if the taxpayer opts for settlement under the GST Amnesty Scheme.
• Invoice-Based Online Refund Filing System: Effective from January 2025, refund claims will be filed invoice-wise directly into Form RFD-01 on the GST Portal, enhancing data accuracy and system validations.

Actionable Steps for Businesses

• Ensure timely filing of GST appeals using Form APL-01 within the prescribed timelines.
• Upload certified copies of orders promptly to avoid delays in acknowledgement.
• Re-file refund applications using the same ARN if a deficiency memo is issued.
• Utilise Form RFD-01W to withdraw refund claims before they are sanctioned or rejected.
• Avoid claiming refunds for payments made before May 2025.
• Consider partial withdrawal of appeals for specific tax periods or issues.
• Opt for the GST Amnesty Scheme to automatically withdraw appeals for eligible periods.
• Prepare for the invoice-based online refund filing system by integrating systems with the GST Portal.

Need Help Navigating the New GST Refund and Appeal Rules?

The recent GST amendments bring important procedural changes that require timely action and precise compliance. To avoid costly delays and ensure your business stays fully compliant with the updated regulations, it’s crucial to get expert guidance. At IndiaFilings, our team of GST professionals is ready to assist you with appeal filings, refund claims, document uploads, and strategic dispute resolution under the new framework. Don’t risk missing deadlines or making procedural errors—connect with IndiaFilings today and streamline your GST compliance with confidence!

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FAQs on 2025 GST Refund and Appeal Amendments

1. What is the new timeline for filing GST appeals under the amended rules?

Taxpayers must file GST appeals using Form APL-01 within 3 months from the date of the order, with a possible extension of 1 month if a valid reason is provided. All appeals must be filed digitally via the GST portal.

2. Is it mandatory to upload a certified copy of the order when filing an appeal?

Yes. The acknowledgement of the appeal will be auto-generated only after uploading a certified copy of the order. Uploading must be done within 7 days to preserve the original appeal filing date.

3. Can I reuse the same ARN if my refund application receives a deficiency memo?

Yes. Under Rule 90(3A), taxpayers can re-file their refund claims using the same ARN without the need to generate a new application, making the refund process more efficient.

4. How can I withdraw a refund claim if I made an error in the application?

You can withdraw refund claims at any time before they are sanctioned or rejected by filing Form RFD-01W.

5. Are refunds allowed for payments made before May 2025?

No. Refunds for any tax, interest, or penalty paid before May 2025 will not be entertained under the new provisions.

6. Is partial withdrawal of appeals allowed now?

Yes. Taxpayers can withdraw appeals for specific tax periods or issues while continuing to contest others, providing more flexibility in dispute resolution.

7. What happens to appeals if I opt for the GST Amnesty Scheme for disputes from July 2017 to March 2020?

Appeals related to these periods will be deemed withdrawn automatically upon opting for the GST Amnesty Scheme.

8.When will the invoice-wise refund filing system come into effect?

The invoice-based refund filing system will be mandatory starting January 2025, requiring refund claims to be filed invoice-wise directly on the GST portal.

RENU SURESH Expert

Updated on: June 2nd, 2025