GSTR-9: Primary Data Source — GSTR-1, GSTR-3B or Books?

GSTR 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.

This is the question the CBIC had to answer by press release, twice. The short answer is that GSTR-9 is filled primarily from GSTR-3B, because that is where tax was actually paid — but which table a transaction lands in depends on when the payment happened, not when the supply was declared.

Per the Press Release dated 3 July 2019: "both FORM GSTR-1 and FORM GSTR-3B serve different purposes. While FORM GSTR-1 is an account of details of outward supplies, FORM GSTR-3B is where the summaries of all transactions are declared and payments are made. Ideally, information in FORM GSTR-1, FORM GSTR-3B and books of accounts should be synchronous." And the Guide adds: "This form would be filled primarily based on Form GSTR-3B filed during the financial year, in which taxes were paid and ITC availed."

Why a mismatch means one of two things

"If the same does not match, there can be broadly two scenarios, either tax was not paid to the Government or tax was paid in excess. In the first case, the same shall be declared in the annual return and tax should be paid, and in the latter all information may be declared in the annual return and refund (if eligible) may be applied through FORM GST RFD-01A."

With one qualification the Guide adds: "there can be certain deviations on account of requirements under the accounting framework followed by the registered person and the taxability criteria under GST Law. It is expected that reconciliation related to such deviation is available with the registered person."

So a difference between books and returns is not automatically an error. Revenue recognition under Ind AS and time of supply under GST diverge legitimately — the requirement is that the reconciliation exists, not that the numbers match.

And GSTN's role is limited. "GSTN is providing data from Form GSTR-1 for reference purposes only which may be used while filing this form."

The three scenarios, from the Press Release of 4 June 2019

The Guide sets out the rule that governs every reporting decision in Parts II and V:

"it is important to understand when tax was paid through Form GSTR-3B for the purpose of declaration of information in Part II and V of Form GSTR-9, irrespective of the fact that when the supply was declared in Form GSTR-1."

Note what distinguishes (a) from (c). They report identically; the difference is that in (c) the money moves through DRC-03 at the time of filing rather than having moved through GSTR-3B earlier.

And the same logic applies to amendments and credit notes:

• invoice issued in the reporting FY but reported and taxes paid in the next FY up to the specified date — Tables 10 and 14;
• an invoice amended upward or downward after 31 March but before the specified date — Tables 10 or 11, and 14;
• a credit note adjusted in the reporting FY — Table 4; adjusted in the next FY up to the specified date — Table 11;
• a credit note that could not be adjusted because there was no output liability against it — refund under excess payment of tax through Form GST RFD-01, per Circular No. 137/07/2020-GST dated 13.04.2020.

The specified date

"Section 39(9) and first proviso to section 37(3) have been amended by the Finance Act, 2022 and notified w.e.f. 1st October 2022 vide Notification No. 18/2022-Central Tax dated 28.09.2022. The outcome… is that from FY 2021-22 onwards, rectification of any omission or incorrect particulars made in Form GSTR-3B / GSTR-1 of the financial year shall be allowed in the relevant return or statement furnished upto 30th November of the next financial year or the date of furnishing annual return for the said financial year, whichever is earlier."

"Whichever is earlier" is the operative limb. A taxpayer who files GSTR-9 on 15 October forecloses corrections for the remaining six weeks — so filing the annual return early can cost the ability to correct.

Section 34(2) was amended identically, so the same date governs when a credit note's effect can still be taken.

The six registers behind the return

The Guide grounds the return in section 35(1) and rule 56, and identifies the records that feed it:

Outward register — determines "the document issued – Tax Invoice, Bill of Supply, Debit Note, Credit Note"; "the type of supply – say B2B, B2C, Exports with/without payment, SEZ supply with/without payment, under RCM, Deemed Supply"; the nature of supply from the place of supply; bundling as regular, composite or mixed; rate from the HSN; and time of supply.

Export register — because "Merely raising an invoice by charging consideration in foreign currency and receiving the consideration in foreign currency does not establish a supply transaction to be in the nature of export." The Guide's illustration: goods ordered by a German company but delivered to Bombay High are "only moving from Mumbai to Bombay High, which is part of India" — not an export, and not reportable in Table 6A of GSTR-1. The register also tracks rule 96A (goods to be exported within 3 months, else tax and interest within 15 days of expiry) and rule 96B (realisation within the FEMA period, from 23.03.2020).

Advance register — because Notification No. 66/2017-CT dated 15.11.2017 removed tax on advances for goods for all except composition taxpayers, while "there is no provision which grant exemption from payment of taxes on receipt of advances, in case of supply of service." Notification No. 50/2023-CT dated 29.09.2023 carved specified actionable claims under section 2(102A) back out of that relief from 01.10.2023.

Import register, reverse charge register — including the payment voucher and self-invoice within 30 days rules — inward register, and stock register, which "will help to identify the blocked credit as per section 17(5)" and "trace deemed supply cases where goods have not been received within time as prescribed under section 143… and goods sent on approval."

Four principles for Table 4 and Table 5

The Guide's own list, which governs the whole of Part II:

• "The outward supplies register should be used as a basis for validating the amounts disclosed in the GST returns."
• "Only those supplies on which tax is payable should be reported . Any supplies which are nil-rated, exempted, non-GST (including no supply) should not be reported."
• "Any outward supplies on which tax is payable on a reverse charge basis by the recipient would not form part of this table."
• "Debit notes and credit notes… should be captured only if the suitable effect of GST is provided in them. In other words, any commercial/accounting credit note which does not contain the charge of GST should not be adjusted."

And one that is easily missed: "Any supply of capital assets is to be carefully verified… as it is a Balance Sheet item and valuation needs to be derived separately as per section 18(6). The transaction value of such sale may not be directly available because of loss/profit on the sale of such assets being disclosed separately in Profit and Loss Account."

Unbilled revenue does not appear at all. "Transactions where the goods or services or both have been supplied but the invoice is not issued (i.e. accounting for unbilled revenue) will not appear in Form GSTR-9. It is a part of reconciliation statement."

Key takeaways

• GSTR-9 is filled primarily from GSTR-3B, because that is where tax was paid and ITC availed; GSTR-1 data is provided for reference only.
• A mismatch means either tax not paid — declare and pay — or tax paid in excess — declare and claim RFD-01.
• Legitimate accounting deviations are expected; what is required is that the reconciliation exists.
• Reporting follows when tax was paid, not when the supply was declared: reporting FY → Tables 4 and 9; next FY to the specified date → Tables 10 and 14; unpaid → Tables 4 and 9 with DRC-03.
• The specified date is 30 November of the next FY or the date of filing GSTR-9, whichever is earlier — so filing early forecloses corrections.
• Six registers feed the return: outward, export, advance, import, reverse charge, inward and stock.
• Table 4 takes only supplies on which tax is payable, excludes recipient-RCM supplies, and counts a credit or debit note only if GST is charged on it.
• Unbilled revenue never appears in GSTR-9 — it belongs to the reconciliation statement.

Read next

• GSTR-9 Table 4: Outward Supplies on Which Tax Is Payable
• GSTR-9 Part V: Tables 10 to 14, the Next-Year Corrections
• GSTR-9: Who Must File, and Who Is Exempt

Disclaimer: Positions stated as on 5 September 2026, based on sections 34, 35, 37, 39 and 44 of the CGST Act, 2017, rules 56, 96A and 96B of the CGST Rules, 2017, Notifications No. 66/2017, 18/2022 and 50/2023-Central Tax, Circular No. 137/07/2020-GST and the CBIC Press Releases dated 4 June 2019 and 3 July 2019, as reproduced in the ICAI Technical Guide on GST Annual Return (Form GSTR-9).