GST refunds changed materially in October 2025. Low-risk applications now get 90 per cent of the claim sanctioned provisionally within seven days, on an automated risk score. What has not changed is that most refund applications still fail at the deficiency memo stage, on statements that do not reconcile, and go back to the start of the queue.
Starting at
₹3,999 onwards
GST refund
Exporters, inverted duty structure, excess cash ledger
Timeline
60 days for final sanction; 7 days for provisional
A GST refund arises on exports made under LUT or with IGST paid, on supplies to an SEZ unit or developer, on an inverted duty structure where the input tax rate is higher than the output rate, on an excess balance in the electronic cash ledger, on tax paid in excess or under the wrong head, on deemed exports, and on assessment or appeal orders. The application is made in Form RFD-01. Inverted duty structure claims have grown sharply since the September 2025 rate restructuring, because a rate cut on the output side without a matching cut on inputs is exactly what creates an inversion.
TL;DR
Apply in Form RFD-01 within two years of the relevant date. Low-risk claims filed on or after 1 October 2025 get 90 per cent sanctioned provisionally in Form RFD-04 within seven days. Your risk score is now a commercial variable - clean filing history is what gets you paid in seven days instead of ninety.
Relevant date
The start of the two-year limitation under Section 54(1). Defined separately for each refund category in Explanation 2 to Section 54 - getting it wrong is how claims are rejected as time-barred.
Form RFD-03
A deficiency memo. Not a rejection, but the application closes, the ITC is re-credited and a fresh application is required. The two-year clock does not stop.
Form RFD-04
The provisional sanction order granting 90 per cent of the claim within seven days of acknowledgment, based on the system's risk evaluation.
Rule 89(2)(m)
Requires a CA or CMA certificate where the refund claimed exceeds ₹2 lakh, certifying that the tax incidence has not been passed on.
Under LUT as a refund of accumulated ITC, or with IGST paid where the shipping bill is treated as the application.
Where the input tax rate is higher than the output rate, under Section 54(3)(ii) and the Rule 89(5) formula.
Excess balance in the electronic cash ledger, tax paid in excess or under the wrong head, deemed exports and UIN holders.
01
If your claim is approaching two years, this is the first thing to settle. The relevant date differs by category under Explanation 2 to Section 54.
02
We tie the statements to the returns filed, match the Rule 89(4) or 89(5) turnover to GSTR-3B and assemble the shipping bill, BRC or FIRC evidence. This is where deficiency memos are avoided.
03
Application filed with the applicable statements and, where the claim exceeds ₹2 lakh, the CA certificate under Rule 89(2)(m). Acknowledgment in RFD-02 follows within 15 days.
04
Low-risk claims get 90 per cent in RFD-04 within seven days. Final sanction or rejection in RFD-06 within 60 days of the complete application. We reply to any RFD-08 show cause in RFD-09.
Upload via our secure portal. We pre-check every scan before filing - cuts portal rejections by ~90%.
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