How exports and SEZ supplies go into GSTR-1 Table 6: the LUT, tax paid or not, the shipping bill, and where each lands in Table 12 and GSTR-3B.
Zero-rated means no tax on the supply, and the credit kept
The IGST Act names two zero-rated supplies: an export of goods or services, and a supply to a unit or developer in a Special Economic Zone for its authorised operations. Either is made one of two ways: under a bond or letter of undertaking without integrated tax, or with integrated tax paid and then refunded (sections 16 and 7(5) of the IGST Act, 2017). Which route a business may take has conditions of its own; settle that with your CA before the first shipment, because a return only reports the choice.
What separates a zero-rated supply from an exempt one is the credit. Section 16 of the IGST Act lets input tax credit be taken for making a zero-rated supply, though the supply itself ends up bearing no tax. An exporter under LUT keeps claiming credit on purchases, and credit left unused can be claimed back as a refund.
Both kinds are inter-state supplies whatever the states, so an SEZ unit in your own state is still an inter-state buyer (sections 7 and 8 of the IGST Act, 2017). The only head on them is integrated tax, never central and state tax.
The LUT comes before the first export of the year
To supply without paying integrated tax, you furnish a letter of undertaking, or a bond, before the export, in Form GST RFD-11 on the portal (rule 96A of the CGST Rules). Notification 37/2017-Central Tax of 4 October 2017 opened the LUT to every registered exporter except one prosecuted for an offence in which the tax evaded exceeds ₹250 lakh, who gives a bond instead. Circular 8/8/2017-GST of the same date says an LUT is valid for the whole financial year in which it is tendered, so each financial year needs a new one before the first supply under it. Rule 96A applies the LUT to supplies made without tax to SEZ units as well as to exports.
In the return, a supply under LUT carries no tax, and its row still names a rate. The law says the tax is nil; no circular says which rate the row names. Practice, and the offline tool’s export sheet, write 0%, and fynxIQ does the same in Tables 6A, 6B and 12. Every return with such a supply carries a warning that says so, with the value and the invoice numbers. If the portal ever asks for the applicable rate instead, the warning asks you to tell us.
With tax paid, the shipping bill is the refund claim
When integrated tax is paid on goods exported, there is no separate refund application. Under rule 96 of the CGST Rules the shipping bill is itself the application, once the carrier has filed the export manifest or export report and you have filed a valid GSTR-3B for the month. The export invoices in your GSTR-1 go from the portal to customs, and customs pays the refund.
So the port code, shipping bill number and date in Table 6A matter: customs holds the invoice against its shipping bill, and a refund whose invoice does not find its bill waits until the two agree. An export of services has no shipping bill; its refund is claimed by application on the portal.
The shipping bill is sometimes not in hand when the GSTR-1 is due. The three fields are optional in the JSON, so the invoice can be reported without them and amended in Table 9A of a later month’s return once the bill is issued. On that amendment, made on the EXPA sheet, the export type, with payment or without, cannot change (Returns Offline Tool user manual, GSTN, the amendment worksheets b2ba to b2csa). fynxIQ’s Amendments tab takes such an export amendment, with its port code and shipping bill.
The invoice carries the endorsement a proviso to rule 46 of the CGST Rules requires: supply meant for export, or to an SEZ unit or developer for authorised operations, on payment of integrated tax or under bond or letter of undertaking without it. fynxIQ does not see the invoice’s wording; it reads the supply type from your register or Tally voucher, and the two should agree.
Table 6 has three rows, and one of them is not zero-rated
Table 6 of the GSTR-1 splits these supplies three ways:
- 6A, exports: one entry per invoice, marked with payment or without, with the port code, shipping bill number and date for goods, and one item per rate. Any tax is integrated tax.
- 6B, supplies to SEZ units and developers, with payment or without, against the unit’s GSTIN. In the JSON the portal takes, they sit in the same b2b section as Table 4, told apart by invoice type: SEWP with payment, SEWOP without.
- 6C, deemed exports: supplies notified under section 147 of the CGST Act by Notification 48/2017-Central Tax of 18 October 2017, such as goods supplied to an export-oriented unit or against an advance authorisation. The goods never leave India, and the supply is not zero-rated: tax is charged like any domestic sale, and a refund of it is a separate claim. In the JSON they are b2b invoices of type DE.
Table 12 and GSTR-3B carry the same supplies again
Table 12, the HSN summary, has a B2B tab and a B2C tab, and the portal validates each against its own supply tables. Supplies to SEZ units (6B) and deemed exports (6C) belong in the B2B tab, because the buyer is registered; exports (6A) belong in the B2C tab, because a foreign buyer is not (GSTN advisory on HSN validations in Table 12 of GSTR-1, 8 January 2025).
In GSTR-3B, zero-rated supplies have a row of their own, 3.1(b), apart from ordinary taxable supplies in 3.1(a). The portal fills 3.1(b) from Tables 6A and 6B and the notes and amendments on them, and puts 6C in 3.1(a), since a deemed export is taxed like a domestic sale (GSTN advisory on auto-population of details in Form GSTR-3B from Form GSTR-1 and GSTR-2B, 5 December 2020). Integrated tax paid on an export or SEZ supply is shown in 3.1(b) and paid with the month’s other tax; a supply under LUT sits there with its value and no tax.
fynxIQ builds Table 12 and its GSTR-3B draft on the same split, so the draft can be held against the portal’s own GSTR-3B row by row.
fynxIQ reads them from your own files and checks each one
An export or SEZ supply comes into fynxIQ from your own sales register, a TallyPrime Day Book or the offline tool’s workbook. In the column mapper, the Export or SEZ field is a column, or one value typed for every row: Regular (or blank), Export with payment, Export under LUT, SEZ with payment or SEZ without payment; the port code, shipping bill number and date have fields of their own. In a Day Book, a party outside India is an export, a party registered as SEZ is an SEZ supply, and a voucher with no tax is under LUT or bond. In the workbook, the exp sheet is Table 6A and the b2b sheet’s invoice type carries 6B and 6C. The marketplace readers and the photographed-bill reader never mark a supply zero-rated.
An export’s place of supply is written as 96, outside India, whatever state the row names, and every export and SEZ supply carries integrated tax only. Then the checks. A blocker holds the GSTR-1 JSON download; a warning does not.
- A register row that says export or SEZ but not whether tax was paid is left out and blocks the return, because the table and the refund route turn on it. So does a row that says deemed export: a deemed export comes in only from the workbook, or as an amendment typed on the Amendments tab.
- A row marked under LUT or bond that charges tax is left out and blocks the return; which of the two it was is not guessed.
- A supply to an SEZ unit with no valid GSTIN blocks the return, and so does an SEZ invoice or note that carries central and state tax.
- A port code that is not six letters and digits, like INDEL4, or a shipping bill number that is not three to fifteen digits, blocks the download, because the portal’s upload would refuse it.
- Supplies under LUT or bond written at 0% raise the warning described above.
They go to Tally invoice by invoice
Exports and SEZ supplies go to Tally one voucher per invoice or note, to sales ledgers of their own, one per rate, with the port code and shipping bill on each export voucher when your file gives them. Each export customer needs its country, as Tally’s country list spells it; fynxIQ suggests none rather than guess. No voucher can say LUT: TallyPrime reads it from the LUT or bond details on the company’s GST registration for the voucher’s date, and the screen tells you to set those before importing. We imported these vouchers into a TallyPrime 7.1 company; import into a copy of yours the first time.
fynxIQ does not furnish an LUT or know whether you have one: the supply type on each row is your word for it. It claims no refund and has no connection to customs or the portal. It prepares the JSON; you upload it and file with your DSC or EVC.
Try it on your own figures with the free GSTR-1 JSON validator.
Which file to download, and from where: the list for each marketplace and the GST portal.
By Raunak Pathak, founder of fynxIQ, who files GST returns on it. Last updated 23 September 2026. This is general information about how GST returns work, not advice about your particular return.