IGST Refund explained: this guide covers what it means, who it applies to, the step-by-step process, documents required, fees, due dates and penalties in India — so you can stay compliant with confidence and avoid costly mistakes.
When an IGST refund on exported goods does not arrive, exporters tend to blame Customs. Very often the claim never reached Customs, because GSTR-1 Table 6A and GSTR-3B do not agree. This article works through the five checkpoints in order, so you can find the break before you write to anyone.
Under Rule 96, the refund is automatic only if every link holds: Table 6A of GSTR-1 carries correct shipping bill details, GSTR-3B Table 3.1(b) shows at least as much IGST as Table 6A, the EGM is filed, the shipping bill validates (SB000), and the bank account registered with Customs is validated by PFMS. A break anywhere stops the refund. Fix Table 6A errors through Table 9A of a later GSTR-1. If Customs is holding the refund under Rule 96(4), the fix is different.
Checkpoint 1: Is GSTR-3B consistent with Table 6A?
The GST portal sends export records to Customs only after GSTR-3B for the period is filed. It also checks that the IGST paid on exports in Table 3.1(b) is not less than the IGST claimed in Table 6A. The ICAI Handbook describes two mistakes that fail this check:
- IGST on exports reported as IGST on domestic inter-State supplies in GSTR-3B; and
- IGST short-paid in GSTR-3B against the liability declared in GSTR-1.
Either way, "the transmission of records from GSTN to Customs EDI system has not taken place", so there is nothing for Customs to process. The portal now auto-populates Table 6A (including Table 9 amendments) into 3.1(b), which reduces the risk, but older periods and manual overrides still cause gaps.
Illustration: Table 6A shows export IGST of ₹4 lakh for June. In GSTR-3B, ₹3 lakh was reported in 3.1(b) and ₹1 lakh went into 3.1(a) as a domestic supply. The ₹4 lakh claim fails the check, and no June export record reaches Customs.
The special relief allowed by Customs circulars for this problem covered FY 2017-18 to FY 2020-21 only. For later periods, correct the position in your returns.
Checkpoint 2: Are the shipping bill details in Table 6A correct?
Table 6A must carry the port code, shipping bill number and date for each export invoice, along with the invoice number, value and IGST, all matching the shipping bill. The Handbook says that where these particulars are "either not available or wrongly quoted", the only way out is to amend them in Table 9A of a later GSTR-1 using the shipping bill particulars.
If you are unsure what is wrong, the Customs response code will tell you. See IGST refund error codes and, for invoice-number errors, SB005 explained.
For help tracing a large backlog of unpaid shipping bills, see our IGST refund on exports with payment service.
Checkpoint 3: Has the EGM been filed and linked?
Under Rule 96(1)(a), the shipping bill counts as a refund application only when the carrier files the departure manifest, export manifest or export report. Cargo from inland ICDs, especially LCL cargo, often shows SB006 (gateway EGM not available). This is fixed by the shipping line, the custodian and Customs, not in your returns.
Checkpoint 4: Is the bank account registered with Customs and validated by PFMS?
Rule 96(3) credits the refund to the bank account in your registration particulars and as intimated to Customs. The Handbook records that the refund is credited to the account registered with Customs even if it differs from the GST registration. That account must be validated by PFMS, and the validation status is visible in the Customs system. An account that has not been validated, or has been invalidated, stops the payment even after the shipping bill validates. Exporters are also advised not to change bank accounts often. See IGST refund bank account change on ICEGATE.
Checkpoint 5: Is the refund being withheld?
Rule 96(4) requires Customs to withhold the refund where:
| Clause | Ground |
|---|---|
| (a) | The jurisdictional GST Commissioner asks for it under section 54(10) or 54(11) |
| (b) | Customs finds the goods were exported in violation of the Customs Act |
| (c) | On data analysis and risk parameters, verification of the exporter's credentials, including ITC, is considered essential |
Under Rule 96(5A)/(5B), withheld claims are sent to the GST officer as a system-generated RFD-01, which is deemed to be the application from the date of transfer, and are then processed under Rule 89. From that point the claim follows the GST refund process, not the Customs one. Risk-flagged exporters have a specific verification procedure, explained in IGST refund withheld: risky exporter verification.
A quick diagnostic table
| Symptom | Most likely break | Fix |
|---|---|---|
| No record visible at Customs | Checkpoint 1: GSTR-3B not filed, or 3.1(b) less than 6A | Correct GSTR-3B reporting and payment |
| SB001 or SB005 | Checkpoint 2: Table 6A particulars | Table 9A amendment |
| SB002 or SB006 | Checkpoint 3: EGM | Carrier, custodian and Customs |
| SB000 but no money | Checkpoint 4: scroll or PFMS | Bank account validation with Customs |
| RFD-01 appears on GST portal unexpectedly | Checkpoint 5: withholding transferred | Respond to the GST officer under Rule 89 |
Time limits while you fix it
Under Rule 96(1), a mismatched application is deemed filed on the date the mismatch is fixed. The two-year limit under section 54 runs from the date the goods left India. GSTR-1 amendments must be made by the earlier of 30 November after the financial year ends and the annual return date. Leaving a Table 6A error for a year can make it unfixable through returns.
Need help tracing an unpaid IGST refund?
We take your export register, GSTR-1, GSTR-3B and ICEGATE data, find exactly which checkpoint failed for each shipping bill, and fix the returns, the EGM follow-up or the bank validation. Start at IGST refund on exports with payment. For LUT-based claims instead, see GST refund on exports, and for every other refund type, our GST refund service.
Key takeaways
- A missing IGST refund is often a GST-return problem, not a Customs one.
- GSTR-3B 3.1(b) must show at least as much export IGST as GSTR-1 Table 6A, or nothing is transmitted.
- Table 6A must carry correct shipping bill number, date and port code. Fix errors via Table 9A.
- EGM errors need the carrier. Bank errors need PFMS validation of the account registered with Customs.
- Withheld claims under Rule 96(4)(a)/(c) move to the GST officer as a system-generated RFD-01.
Read next
- Refund of IGST paid on exports: shipping bill route
- IGST refund status on ICEGATE
- GST refund scroll status meaning
- Common reasons for GST refund rejection and remedies
Disclaimer: Positions stated as on 30 September 2026, based on the CGST Act and Rules as amended, the Finance Act 2026, and the ICAI Handbook on Refunds under GST (January 2026). Verify current notifications before filing.