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For an Indian GST-registered exporter of goods, reconcile every export invoice to GSTR-1 Table 6A and its shipping bill or bill of export before claiming a refund. Match the invoice number and date, port code, customs document number and date, invoice and taxable values, and the IGST-paid treatment. Then confirm that the relevant GSTR-3B was validly furnished and that the export-manifest condition is satisfied. Under Rule 96 of the CGST Rules, an unresolved shipping-bill/GSTR-1 mismatch delays the date on which an IGST refund application is deemed to have been filed.
What this reconciliation is designed to prove
The purpose is to create one defensible chain from the accounting invoice to the GST return and, for goods, to the customs export record. A refund review should be able to answer three questions for every invoice:
- Did the invoice in the sales register appear correctly in the filed outward-supplies return?
- Does the customs document identify the same export transaction?
- Does the selected refund route match the way GST was treated at export?
This procedure is primarily for exports of goods. Export-of-services claims use different evidence and filing mechanics, so a goods checklist should not be applied to a services claim without adjustment.
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Choose the refund route before checking the data
GST Portal guidance describes exports as generally zero-rated inter-State supplies and identifies two broad choices: export without payment of IGST and seek a refund of eligible unutilized input tax credit, or pay IGST and seek a refund of the IGST paid after export. The transaction type and the route determine which records matter most.
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| Export situation | Tax paid at export | Refund sought | Principal mechanism to verify |
|---|---|---|---|
| Goods exported with IGST payment | IGST paid | IGST paid on the exported goods | Rule 96 process using the export invoice in GSTR-1, shipping-bill data, a valid GSTR-3B and the export-manifest/export-report condition |
| Goods exported under a Letter of Undertaking | No IGST paid at export | Eligible unutilized ITC | LUT in Form GST RFD-11 and the refund evidence and application requirements under Rule 89 |
| Services exported without payment of tax | No IGST paid at export | Eligible unutilized ITC | LUT where applicable and the Rule 89 refund procedure; supporting evidence differs from a goods shipping-bill record |
| Services exported with IGST payment | IGST paid | IGST paid on exported services | Rule 96 states that the application is made in Form GST RFD-01 under Rule 89; do not use the goods shipping-bill workflow as a substitute |
The table is a route-selection framework, not an eligibility opinion. Eligibility, net ITC, realization conditions and supporting documents depend on the transaction facts and the current portal procedure.
Build an invoice-level control population
Start with the export sales register for the tax period, not with a portal download. Assign one row to each export tax invoice and retain its accounting and customs references. Include credit notes, debit notes and any amended export invoice records in a way that makes the original and correction traceable.
Minimum fields for each invoice row
| Field | Why it matters | Primary record |
|---|---|---|
| Tax invoice number and date | Establishes invoice identity across accounting, GSTR-1 and customs records | Tax invoice and sales register |
| Total invoice value | Shows whether the value reported to GST and customs is the same transaction value | Invoice, sales register and GSTR-1 |
| Taxable value | Supports the outward-supply amount used for the return and the refund route | Invoice and GSTR-1 |
| IGST treatment | Confirms whether the invoice belongs in an IGST-paid refund population or a no-payment/LUT population | Invoice tax treatment and GSTR-1 selection |
| Port code | Connects the GST export entry with the customs location | Shipping bill or bill of export and GSTR-1 |
| Shipping-bill or bill-of-export number and date | Provides the customs identifier used for a goods-export refund | Customs document and GSTR-1 |
| GSTR-1 filing period and amendment reference | Shows when the invoice was first reported and where a later correction was made | Filed GSTR-1 and any amendment section |
| GSTR-3B filing status | Rule 96 ties the deemed filing condition to a valid return | GST Portal filing status |
Do not silently drop an invoice because a shipping-bill number is missing. Mark the row as pending, retain the invoice in the population and document the follow-up needed.
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- Freeze the population. Define the tax period and export route, then extract every relevant export invoice from the sales register. Record invoice number, date, values, tax treatment and the expected customs document. Keep a separate status column such as matched, amendment required, customs detail pending or investigation required.
- Compare each row with GSTR-1 Table 6A. Table 6A is the export-invoice section identified in the GST Portal’s GSTR-1 instructions. Confirm that each invoice appears once, in the correct period or amendment, and that the invoice number, date, total value, taxable value and GST-payment selection agree with the source invoice. Investigate both omissions and duplicates.
- Review e-invoice population where applicable. E-invoice details may be auto-populated into GSTR-1, and the GST Portal allows those details to be downloaded and reviewed. Treat the downloaded data as a review source, not as proof that the accounting and customs fields are correct. Compare the auto-populated values with the signed invoice and the sales register.
- Attach the customs record to the same invoice row. Enter the port code, shipping-bill or bill-of-export number and date from the customs document. Check that the customs invoice reference points to the same export invoice rather than to a packing-list number, internal order number or a different commercial invoice.
- Test the value fields. Compare total invoice value and taxable value separately. A matching taxable value does not prove that the total invoice value is correct, and a rounding difference should not be dismissed until the cause is identified in the source documents and reporting format.
- Test the IGST-paid selection. The return entry must reflect whether IGST was actually paid at export. An invoice reported as tax-paid while the transaction was made under LUT, or reported as without payment when IGST was paid, places it in the wrong refund population and requires correction before the claim is prepared.
- Check the mismatch condition under Rule 96. Compare the shipping-bill data transmitted through customs with the outward-supplies data reported by the exporter. If the invoice identity, value or linked export details do not agree, classify the row as unresolved and correct the relevant GST data rather than assuming the system will overlook it.
- Confirm the return and export status prerequisites. Verify that the applicable GSTR-3B has been validly furnished. Also verify the relevant export-manifest or export-report status required for the goods-export process. The available statutory guidance does not provide a universal line-by-line GSTR-3B table crosswalk, so do not invent one; use the claim route and current portal instructions to determine the detailed return checks.
- Handle late customs details through amendment. GST Portal guidance permits export invoice details to be filed in GSTR-1 when shipping-bill details are not yet available. When those details are received later, report them in the amendment section of GSTR-1 for the month in which they are received. An amendment does not excuse a separate mismatch: any discrepancy relevant to Rule 96 must still be rectified.
- Lock the evidence trail. Save the final filed GSTR-1, amendment acknowledgement, customs document, return-filing status and the reconciliation file that shows who reviewed each exception. Freeze the version used to prepare the refund so a later accounting edit cannot make the submitted claim irreproducible.
Field-by-field tests and common failure points
| Test | Pass condition | Typical failure | Correction approach |
|---|---|---|---|
| Invoice number | One exact invoice identity appears in the register, GSTR-1 and customs linkage | Prefix, slash, leading-zero or amended number differs | Trace the legal invoice and report the correction in the appropriate GSTR-1 amendment location |
| Invoice date | Date agrees with the invoice used for the export and the reported transaction | Accounting date and return date are confused, or an amendment carries the wrong date | Use the tax invoice as the source and document why any permitted reporting-period difference exists |
| Port code | GSTR-1 port code identifies the customs location on the shipping document | Old code, typographical error or a different port from the final export | Validate against the customs record and amend the GST entry where the portal permits |
| Shipping-bill or bill-of-export number and date | Number and date point to the same exported goods and are reported for the relevant invoice | Details were unavailable when GSTR-1 was filed, or a number from another invoice was entered | Use the later amendment process for newly received details and correct any wrong linkage |
| Total invoice value | Reported value can be reconciled to the commercial invoice and customs data | Currency conversion, freight treatment or a data-entry error creates a difference | Identify the source of the difference and correct the record that is wrong; retain the calculation or document supporting the conversion |
| Taxable value | Taxable value in GSTR-1 agrees with the invoice’s GST basis | Taxable and total values are transposed or a credit note is omitted | Correct the return entry and ensure the refund population reflects the net, legally reportable transaction |
| GST-payment indicator | Selection agrees with the actual IGST payment or LUT treatment | Invoice is placed in the wrong refund route | Correct the classification before filing; do not claim IGST paid on a no-payment export |
How Rule 96 changes the filing date
For an IGST refund on exported goods, Rule 96 does more than describe a data check: it determines when the application is deemed to have been filed. Rule 96(1)(b) states:
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“Provided that if there is any mismatch between the data furnished by the exporter of goods in Shipping Bill and those furnished in statement of outward supplies in FORM GSTR-1, as amended in FORM GSTR-1A if any, such application for refund of integrated tax paid on the goods exported out of India shall be deemed to have been filed on such date when such mismatch in respect of the said shipping bill is rectified by the exporter;”
In practical terms, a shipping bill that does not match the exporter’s GSTR-1 data is not ready merely because the invoice was originally reported. The relevant deemed filing date waits until the exporter rectifies the mismatch for that shipping bill. Keep evidence of the correction, including the amended return period and acknowledgement, with the refund workpapers.
Rule 96 also connects the goods-export process with a valid GSTR-3B and the export-manifest or export-report condition. A portal status that appears to show an invoice is present does not replace those statutory prerequisites.
Late shipping-bill information: the correct treatment
The GST Portal’s export FAQ recognizes that shipping-bill details may not be readily available when GSTR-1 is filed. You may report the export invoice without those details initially. Once the number and date are received, enter them in the amendment section for the month in which they are received.
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What to retain while the details are pending
- The original invoice and export register row.
- Evidence that the goods were intended for export and the customs document was awaited.
- A follow-up owner and due date for obtaining the shipping-bill or bill-of-export details.
- The later amendment acknowledgement and the revised GSTR-1 extract.
If the later customs details reveal that the original invoice number, value or port code was wrong, treat the issue as a substantive mismatch and correct all affected fields, not just the newly available number.
Documents to assemble before preparing the claim
For a goods-export reconciliation, have one controlled folder or electronic file set containing:
- The export invoice register and copies of the tax invoices.
- The filed GSTR-1 for the relevant periods, including amendment entries and acknowledgements.
- Shipping bills or bills of export showing the port, number and date linked to each invoice.
- Evidence of the applicable export-manifest or export-report status.
- Filed GSTR-3B status for the relevant period.
- The route decision: IGST-paid export or export without payment under LUT.
- Form GST RFD-11 where the export was made under a Letter of Undertaking.
- The reconciliation file, exception explanations and reviewer sign-off.
Rule 89 identifies a statement containing shipping-bill or bill-of-export numbers and the relevant export invoice numbers and dates as evidence for an export-of-goods refund application. That statement is part of the evidence framework; it should not be treated as a substitute for checking the underlying invoice, return and customs records.
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Do not use the presence of a zero-rated invoice as a reason to apply the goods workflow to every export. Goods have a shipping bill or bill of export and a port code. Services generally do not have those customs fields, and their refund evidence and eligibility tests follow the applicable Rule 89 procedure.
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For exports without payment of tax, the GST Portal identifies Form GST RFD-11 as the LUT form. For services on which IGST was paid, Rule 96 points to Form GST RFD-01 under Rule 89. The exact supporting records, realization evidence and calculation depend on the service transaction and the route selected, so a services team should create a separate control matrix rather than leaving customs columns blank in a goods template.
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Invoice is missing from Table 6A
Confirm that the invoice was not reported under another number, in another period or through an amendment. If it is genuinely omitted, correct the GSTR-1 position before treating the population as complete. Do not rely on a customs record alone to establish that the GST return is correct.
Invoice appears twice
Identify whether one entry is an amendment of the other or a true duplicate. A duplicate can overstate outward supplies and distort the refund population; preserve the correction trail rather than deleting a row from the working file without explanation.
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Stop the claim for that row. Compare the commercial invoice, customs invoice reference and GSTR-1 entry, then correct the incorrect linkage through the available amendment process. The Rule 96 mismatch consequence applies until the relevant shipping-bill data is rectified.
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Values differ between GST and customs
Separate currency conversion, freight or other valuation causes from a simple keystroke error. Reconcile the calculation to the source documents and amend the GST entry if it is wrong. Do not create an unsupported tolerance merely to force a match.
IGST treatment is wrong
Determine whether IGST was actually paid or the export was made under LUT. Correct the return classification and route the invoice to the appropriate refund population. A refund claim cannot be made coherent by changing only the spreadsheet status.
GSTR-3B is not validly furnished
Keep the invoice in a pending status and resolve the return-filing issue before relying on the Rule 96 deemed-filing condition. The available rule text does not provide a universal substitute where the return prerequisite is absent.
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Retain the customs evidence and monitor the status. Treat the row as not ready for the goods IGST refund process until the required export-report condition is met, unless current official guidance provides a specific alternative for the case.
Controls that make the reconciliation defensible
- Use one immutable invoice key. Keep the legal invoice number and date as the primary key; store internal order and shipment references as secondary fields.
- Separate source and correction columns. Preserve the original filed value, the corrected value and the reason for amendment instead of overwriting history.
- Reconcile at invoice level before aggregating. An aggregate total can hide one omitted invoice and one duplicate invoice that happen to offset.
- Record route selection explicitly. Mark each row as IGST-paid or LUT/no-payment and require a reviewer to approve any change.
- Keep portal downloads dated. Save the GSTR-1 extract and amendment acknowledgement used for the claim so a later portal change does not alter the evidence set.
- Require independent review of exceptions. The preparer should not close a shipping-bill mismatch or change the refund route without a documented second review.
Final readiness decision
An IGST-paid goods export is ready for the Rule 96 refund workflow only when its invoice is correctly reported in GSTR-1 Table 6A, the customs identifiers and values link to that same invoice, any mismatch has been rectified, the relevant GSTR-3B is validly furnished and the export-manifest or export-report condition is satisfied. If any one of those facts is still pending, keep the row out of the ready population and preserve the evidence needed to close it.
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