GST Refund on Exports With Payment of IGST
When you export goods on payment of IGST, your shipping bill itself is treated as the refund application. We reconcile GSTR-1 (Table 6A), GSTR-3B and your ICEGATE data so the automated refund flows through — and we clear holds when it does not.
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What Is Export IGST Refund?
A plain-language view of the IGST-payment refund route before the mechanics.
It is the refund of the IGST you paid on exported goods. Because exports are zero-rated, that tax comes back to you — and for the payment route, the shipping bill acts as the refund claim, so the refund is processed automatically.
Under Section 16 of the IGST Act, 2017, exports are zero-rated supplies. Section 16(3) lets an exporter pay IGST and claim a refund of the tax paid. Rule 96 of the CGST Rules, 2017 deems the shipping bill filed by an exporter to be an application for refund of the integrated tax, subject to the correct filing of the export return.
Processed jointly by the GST system (GSTN), Customs / ICEGATE and the jurisdictional CBIC officer. The GST portal transmits export invoice and tax data to ICEGATE, which validates it against the shipping bill and EGM.
The refund claim must be made within two years of the relevant date. For export of goods, the relevant date under Section 54 is the date on which the goods leave India (date of export / let-export).
Quick Facts
Is This Service Right for You?
Ideal for
- Merchant and manufacturer exporters shipping goods on IGST payment
- Exporters whose refunds are stuck despite a valid shipping bill
- Businesses seeing GSTR-1 vs GSTR-3B export mismatches
- Exporters facing EGM / shipping-bill error codes at ICEGATE
- Those unsure whether Rule 96(10) or Rule 96B applies to them
- Exporters who want the automated route managed end-to-end
You may need this if
- You exported goods and paid IGST on the shipment
- Your refund has not been credited despite filing returns
- ICEGATE shows a hold or an error against your shipping bill
- Your Table 6A figures do not match GSTR-3B
- You received a concessional-rate benefit that may trigger Rule 96(10)
- You want to confirm the correct relevant date and time limit
Not sure if you need this?
Talk to an Expert →Why Exporters Choose the IGST-Payment Route
Exports are zero-rated, so the tax you pay on an export must not stick. The payment-of-IGST route is largely automated — but it only works cleanly when your returns and customs data agree.
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01
Exports Are Zero-Rated
Under Section 16 of the IGST Act, export of goods is a zero-rated supply. Any IGST charged on the export shipment is refundable so that domestic tax is not exported along with the goods.
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02
No Separate Application
Under Rule 96, the shipping bill is deemed to be the refund application. There is no RFD-01 to file for this route — the claim is embedded in your customs and return data.
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03
System-Processed via ICEGATE
Once GSTR-1 Table 6A and GSTR-3B are filed, the data flows to ICEGATE and is matched with the shipping bill and EGM. A clean match triggers the refund without manual intervention.
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04
Faster Working-Capital Recovery
Because the process is automated, a correctly filed claim can be sanctioned without a manual sanction order — freeing blocked IGST back into your cash flow.
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05
Interest on Delay
Where a valid refund is delayed beyond 60 days from a complete application, interest is payable under Section 56 of the CGST Act (6%, or 9% in specified appeal cases).
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06
Clean Compliance Trail
A properly documented export refund keeps your zero-rated turnover, ITC and customs records aligned — reducing the risk of future scrutiny or recovery.
Simple, Transparent Pricing
Custom quote for your case
Fees depend on your business type and scope. Get a clear, itemised quote upfront — no hidden professional charges, government fee billed at actuals.
Who Can Apply?
Eligibility checklist
- The supply is an export of goods that is zero-rated under Section 16 of the IGST Act
- IGST was actually paid on the export shipment (payment route, not LUT)
- A valid shipping bill and Export General Manifest (EGM) have been filed
- GSTR-1 Table 6A carries the correct export invoice and IGST details
- GSTR-3B for the same period reports and pays the corresponding IGST
- The exporter is not disentitled under Rule 96(10) / Rule 96B for the period
Everything You Need. One Professional Team.
Refund Feasibility Review
Confirm the shipment qualifies for the payment route and check for Rule 96(10)/96B disqualifiers.
Return Reconciliation
Match GSTR-1 Table 6A export invoices against GSTR-3B tax paid and your shipping-bill data.
ICEGATE Validation
Cross-check the invoice, shipping bill and EGM so the customs system can validate the claim.
Error & Hold Diagnosis
Identify the ICEGATE error code or hold reason (SB005, EGM error, mismatch) behind a stuck refund.
Corrective Filing
Amend Table 6A, file the required corrections and coordinate on shipping-bill / EGM fixes.
Officer Coordination
Represent your case with the jurisdictional or customs officer where manual intervention is needed.
Rule 96(10) / 96B Advisory
Assess exposure where concessional-rate imports or non-realisation trigger recovery or restriction.
Status Tracking
Track the refund scroll and sanction status until the amount is credited to your account.
What You’ll Receive
Documents & Data Needed for the IGST Refund
For the payment route, most of the claim is built from data you have already filed — the shipping bill, GSTR-1 Table 6A and GSTR-3B. These records help us confirm the match and resolve any hold.
Export & Customs Documents
- Shipping bill(s) for the export shipment
- Export invoice(s) with IGST charged
- Bill of lading / airway bill
- Export General Manifest (EGM) reference
GST Return & Registration
- GSTIN and GST portal access
- GSTR-1 with Table 6A export details
- GSTR-3B for the relevant tax period(s)
- IEC (Import Export Code)
Realisation & Banking
- Bank account details for the refund credit
- BRC / FIRC or realisation proof (where called for)
- AD-code registration at the port
- Reconciliation of invoice value vs realised value
Table 6A must match the shipping bill
The export invoice number, value, IGST amount and shipping-bill / port details in GSTR-1 Table 6A must match what was filed with Customs. A mismatch is the most common reason the refund does not transmit.
GSTR-3B must actually pay the IGST
The IGST shown as paid on exports in GSTR-3B (Table 3.1(b)) must reconcile with the IGST declared in Table 6A. If 3B under-reports, the system holds the refund.
EGM filing is essential
ICEGATE validates the shipping bill against the Export General Manifest. A missing, late or erroneous EGM is a frequent cause of a stuck refund and needs a carrier / customs correction.
Rule 96(10) & 96B
If you availed certain concessional-rate / exemption benefits on inputs, Rule 96(10) may bar the payment route; and Rule 96B allows recovery where export proceeds are not realised within the FEMA period. Both need to be assessed before claiming.
Don’t have all the documents?
We’ll identify what your case needs →How the IGST-Payment Refund Works
The claim is embedded in your returns and customs filings — the key is getting all three data sets to agree.
Export on payment of IGST
Ship the goods, raise a tax invoice charging IGST, and file the shipping bill at the port. Paying the IGST is what puts you on this route.
File GSTR-1 with Table 6A
Declare each export invoice in Table 6A of GSTR-1 with the correct value, IGST and shipping-bill / port details for the relevant period.
File GSTR-3B and pay the IGST
Report and discharge the corresponding IGST on exports in GSTR-3B so the tax paid reconciles with Table 6A.
Data transmits to ICEGATE
The GST portal sends your export invoice and tax data to Customs / ICEGATE, which validates it against the shipping bill and EGM.
System matches and generates the scroll
On a clean match, Customs generates the refund scroll — no separate RFD-01 or manual sanction is needed for this route.
Refund credited or hold resolved
The refund is credited to your registered bank account. If a mismatch, EGM error or Rule 96 issue holds it, we diagnose and correct the specific cause.
How Long the IGST Refund Takes
| Stage | Expected Time |
|---|---|
| Return filing → data transmission to ICEGATE | After GSTR-1 & GSTR-3B are filed |
| ICEGATE validation & scroll generation (clean match) | System-processed, no manual sanction |
| Refund held for mismatch / EGM / SB error | Until the specific error is corrected |
| Statutory outer limit to make the claim | Within 2 years of the relevant date |
The relevant date is the date the goods leave India. Where a valid refund is delayed beyond 60 days of a complete claim, interest is payable under Section 56 of the CGST Act (6%, or 9% in specified appeal cases). Actual timing depends on the accuracy of the match and any customs correction required.
Doing It Yourself vs TaxClue
Doing It Yourself
- Confirm whether the payment route or LUT route applies to your shipment
- Reconcile Table 6A, GSTR-3B and shipping-bill data line by line
- Decode ICEGATE error codes (SB005, EGM errors) yourself
- Chase carriers and Customs for EGM corrections
- Assess whether Rule 96(10) or 96B disqualifies you
- Compute the relevant date and the two-year limit
- Represent a held refund before the officer
With TaxClue
- Route confirmed and eligibility screened upfront
- Full GSTR-1 / GSTR-3B / shipping-bill reconciliation done for you
- Error codes diagnosed and mapped to a fix
- EGM and shipping-bill corrections coordinated
- Rule 96(10) / 96B exposure assessed before claiming
- Relevant date and time limit tracked
- Officer and customs representation handled
Skip the guesswork.
Let an expert handle it →Common Mistakes That Delay Your Application
TaxClue reviews your documents before filing to reduce avoidable errors.
Penalties & Consequences
What is at stake if you do not comply
- GSTR-1 Table 6A not matching the shipping bill stalls the auto-refund at ICEGATE
- IGST under-reported in GSTR-3B versus Table 6A holds the refund
- A missing, late or erroneous EGM keeps the refund stuck at Customs
- A Rule 96(10) bar can make an already-refunded amount recoverable
- The IGST refund lapses if not claimed within 2 years of the relevant date
Regulatory Updates 2025–26
- 2025: GST refund applications are filed in Form RFD-01 within 2 years of the relevant date under Section 54.
- 2025: Exporters file a Letter of Undertaking (Form RFD-11) afresh each financial year to export without paying IGST.
Why Businesses Choose TaxClue
Refund Specialists
A team that works export IGST refunds and ICEGATE holds every day.
Reconciliation First
We fix the GSTR-1 / GSTR-3B / shipping-bill match before anything else.
Error-Code Fluent
We map SB005, EGM and mismatch errors straight to the correction.
Rule 96 Aware
We screen Rule 96(10) and 96B exposure so a claim does not backfire.
Customs Interface
We coordinate with Customs and carriers on EGM and shipping-bill fixes.
Tracked to Credit
We follow the scroll and sanction status until the money lands.
Your Documents Deserve Professional Care
- Export, banking and tax data handled by professionals under confidentiality
- Access limited to the team working on your refund file
- Communication over secure digital channels
- Records retained only as long as needed for the refund and compliance
Frequently Asked Questions
Do I need to file RFD-01 for an export refund with IGST paid?
How is the IGST export refund processed?
What is the relevant date for an export-of-goods refund?
Why is my IGST refund stuck even though I filed my returns?
What is an EGM and why does it matter?
What is Rule 96(10) and could it affect my refund?
What is Rule 96B?
Do I get interest if the refund is delayed?
Can I switch between the IGST-payment route and the LUT route?
What if my Table 6A and GSTR-3B figures do not match?
Is there any government fee to claim this refund?
What documents do I need for the IGST export refund?
Can a merchant exporter claim this refund?
How do I claim a GST refund on exports with payment of IGST?
What is the difference between export with payment of IGST and export under LUT?
What is the SB005 error and how is it resolved?
What is the relevant date and time limit for the IGST export refund?
Can I get a provisional refund on the IGST-payment route?
Official Sources & Legal References
Every regulatory figure on this page — the rule, the relevant date, the time limit and the interest rate — is drawn from primary law and official sources. Verify them directly:
- IGST Act & CGST Act, 2017 — full textSec 16 IGST (zero-rated supply), Sec 54 & Sec 56 CGST (refund & interest) · India Code
- CBIC-GST — CGST Rules & NotificationsRule 96, Rule 96(10) and Rule 96B of the CGST Rules, 2017
- ICEGATE — Customs / IGST refund statusShipping-bill, EGM and IGST refund scroll status
- GST Portal — returns & refundsFile GSTR-1 (Table 6A) and GSTR-3B; track refund status
Related Guides
Refunds Under Sections 54–58
Read guide ArticleFiling RFD-01: A Guide
Read guide ArticleZero-Rated Supply (Sec 16 IGST)
Read guide ArticlePlace of Supply: Import & Export
Read guide ArticleWhy Refunds Get Rejected
Read guide ArticleHow ITC Matching in GSTR-2B Works
Read guide ArticleTax Invoice: Mandatory Fields
Read guide ArticlePayment & Electronic Ledgers
Read guideExport IGST Refund Resources — All Free
Unlock Your Blocked IGST Export Refund
From GSTR-1 / GSTR-3B reconciliation to ICEGATE holds, EGM errors and Rule 96(10)/96B exposure — our experts manage the full IGST-payment refund. Free consultation, no obligation.