Ques: We have differences between books of accounts and GST returns (GSTR-1 / GSTR-3B) due to technical issues such as e-invoice duplication / wrong classification. The question is whether such differences can be corrected in GSTR-9 or should be reported only through GSTR-9C.

Ans:

Differences between books of accounts and GST returns (GSTR-1 / GSTR-3B) arising due to technical or reporting issues such as e-invoice duplication, wrong tax classification, or similar errors cannot be corrected through GSTR-9, except to the very limited extent permitted within the structure of the annual return. GSTR-9 is primarily a consolidation statement, and while it allows certain summary-level adjustments or disclosures, it does not permit revision of tax liability or ITC already reported in GSTR-1 or GSTR-3B.

Accordingly, where such differences cannot be rectified in monthly/quarterly returns due to lapse of time or system constraints, the correct and compliant approach is to report and explain them through GSTR-9C, which is specifically designed as a reconciliation statement between audited books and GST returns. In GSTR-9C, the differences arising due to e-invoice duplication, wrong classification, or other technical issues should be clearly identified, quantified, and explained in the relevant reconciliation tables, with proper narration. Any additional tax liability arising from such reconciliation (if any) would be payable through DRC-03, whereas differences that are merely reporting or timing in nature and do not impact tax liability can be reconciled without payment.

In summary, GSTR-9 should reflect the figures as finally reported in GSTR-1 and GSTR-3B, and GSTR-9C is the appropriate and legally intended forum to disclose, reconcile, and explain differences between books and returns, ensuring transparency and audit defensibility.

Ques: We seek clarification on the filing of GSTR-9C in a scenario where an entity is registered under multiple GSTINs (same PAN).
Our queries are as under:
1. In case a taxpayer has more than one GSTIN, is it permissible to file a consolidated GSTR-9C for all GSTINs together?
2. If consolidation is allowed, does the taxpayer need to:
o File only one consolidated GSTR-9C, or
o File separate consolidated GSTR-9C reports for each GSTIN?
3. Alternatively, Can we file GSTR-9C GSTIN-wise, wherein:
o Turnover is reported GSTIN-wise, and
o Purchases and other details are also shown separately for each GSTIN, matching the respective GSTR-9 and books of accounts?
Kindly Provide correct and compliant approach, along with any relevant legal references or practical considerations, if available.
Looking forward to your clarification.

Ans:

The correct and compliant position under GST is that GSTR-9C is required to be filed strictly GSTIN-wise and not on a consolidated PAN basis, even where multiple GST registrations exist under the same PAN.

Form GSTR-9C is a reconciliation statement between the Annual Return (GSTR-9) and the audited financial statements, and since GSTR-9 itself is filed separately for each GSTIN, the reconciliation statement must necessarily correspond to that particular GSTIN. The format of GSTR-9C is GSTIN-specific, and the GST portal also permits filing only one GSTR-9C per GSTIN per financial year, making a consolidated filing for multiple GSTINs legally and technically impermissible.

Clarification on your specific queries:

1. Consolidated GSTR-9C for all GSTINs together:
   Not permissible. There is no provision under the CGST Act, Rules or Form GSTR-9C allowing a single consolidated GSTR-9C for all GSTINs under the same PAN.
2. Filing one consolidated GSTR-9C or separate consolidated reports:
   Neither is allowed. Even if books of accounts are maintained centrally at PAN level, GSTR-9C cannot be filed on a consolidated basis, whether as one report or multiple consolidated reports.
3. GSTIN-wise filing of GSTR-9C (Correct approach):
   This is the only legally correct and compliant method.
   Accordingly:
   • Separate GSTR-9C must be filed for each GSTIN
   • Turnover must be reported GSTIN-wise, matching the respective GSTR-9
   • ITC, purchases, tax paid, reversals and adjustments must also be allocated GSTIN-wise
   • Audited financial statements may be common at PAN level, but a reconciliation statement / working allocation must be prepared to map figures to each GSTIN

Practical considerations:
PAN-level audited financials can be attached for each GSTIN
Allocation workings (branch-wise turnover, expense ratios, etc.) should be maintained
Reconciliation differences should be explained GSTIN-wise
This approach avoids portal rejection, audit objections and future litigation

Conclusion:
➡ GSTR-9C must be filed separately for each GSTIN
➡ No consolidated GSTR-9C is permitted under GST law
➡ GSTIN-wise reconciliation aligned with respective GSTR-9 is mandatory

This GSTIN-wise approach is fully aligned with the structure of section 44 of the CGST Act, Rule 80, and the design of Forms GSTR-9 and GSTR-9C, and is the only defensible position in audit or scrutiny.

Ques: Whether Balance sheet and Profit and loss account attached in GSTR-9C should be signed by auditors or without signing of auditor.

Ans: The Balance Sheet and Profit & Loss Account attached with Form GSTR-9C are required to be the audited financial statements, and therefore they should be duly signed by the auditor and the authorised signatory of the entity, wherever audit under any law (such as the Companies Act, LLP Act, or Income-tax Act) is applicable. GSTR-9C itself is a reconciliation statement based on audited accounts, and attaching unsigned or provisional financial statements would defeat its purpose and may invite objections during departmental scrutiny. Accordingly, the financial statements uploaded along with GSTR-9C should be final, audited, and signed, even though the auditor does not certify GSTR-9C in the post self-certification regime.