Preparing Form GSTR-9C often brings to light mismatches between the input tax credit recorded in audited financial statements and the credit claimed through Form GSTR-3B. Accountants spend considerable hours during annual return filing season isolating why expenses in the profit and loss account do not match the figures reported in the annual return. Table 12 captures this reconciliation, while Table 13 requires structured explanations for any remaining variances.
Statutory framework for GSTR-9C Table 12
Section 44 of the Central Goods and Services Tax Act mandates that every registered person whose aggregate turnover exceeds the prescribed threshold must furnish an annual return along with a reconciliation statement. Rule 80(3) of the Central Goods and Services Tax Rules specifies that Form GSTR-9C serves as this reconciliation statement. Tax authorities rely on Table 12 to verify whether input tax credit reflected in the books of accounts aligns with the credit availed in the returns filed during the financial year Central Board of Indirect Taxes and Customs.
Common mistake: Comparing GSTR-2B figures directly against the profit and loss account without factoring in opening and closing provisions, capital goods credits, or expenses booked without GST numbers. Table 12 specifically compares GSTR-9 ITC availed against audited books.
Structure of Table 12 and Table 13
- Table 12A: Enter the total input tax credit availed through GSTR-3B during the financial year.
- Table 12B to 12E: Account for adjustments such as ITC booked in previous years claimed in current year, ITC booked in current year claimed in subsequent year, and ineligible ITC.
- Table 13: Provide reasons for unreconciled differences identified between the adjusted book credit and the claimed return credit.
Worked example: reconciling books and GSTR-9
Consider a manufacturing enterprise in Pune with audited accounts for the financial year. Total input tax credit as per the audited profit and loss account stands at ₹45,50,000, while the total ITC availed in GSTR-3B is ₹44,20,000. The accountant must reconcile this variance of ₹1,30,000 across specific categories.
| Reconciliation Line Item | Amount (₹) | Explanation |
|---|---|---|
| Audited P&L ITC | ₹45,50,000 | Total ITC on inputs, input services, and capital goods in books |
| Less: Ineligible ITC in books | (₹2,50,000) | Blocked credit under Section 17(5) expensed in P&L |
| Add: ITC claimed in current year for prior invoices | ₹1,80,000 | Invoices of previous FY claimed in April to November of current FY |
| Less: ITC carried forward to subsequent year | (₹60,000) | Invoices of current FY claimed in subsequent financial year |
| Reconciled ITC as per Table 12 | ₹44,20,000 | Matches total ITC availed in GSTR-9 Table 8A |
When the final computed figure in Table 12 does not match GSTR-9, Table 13 requires clear explanatory notes. For related guidance on annual return computations, review the GSTR-9 Table 8 reconciliation formula guide and the calculations detailed in GSTR-9 Table 8D lapsed ITC calculation.
When reviewing subsequent year adjustments, cross-verify entries against PURCHASE_REGISTER_2025_26.xlsx and cross-check table totals with GSTR-9 Table 10 and 11 subsequent year amendments.
“The annual return shall be filed in such form and manner as may be prescribed along with a copy of the audited annual accounts and a reconciliation statement, reconciling the value of supplies declared in the return furnished with the audited annual financial statements.” Section 44 of the Central Goods and Services Tax Act, 2017
Related guides
- GSTR-9C reconciliation statement
- GSTR-9 Table 7 Rule 37 ITC reversal: 180 days non-payment and reclaim
- GSTR-9 Table 14: reporting differential tax paid in cash with Form DRC-03 reconciliation
- ASMT-10 reply for GSTR-9 Table 8D mismatch: format and legal defence
Frequently asked questions
What is the primary purpose of GSTR-9C Table 12?
Table 12 of Form GSTR-9C reconciles the total input tax credit availed in the annual return GSTR-9 with the input tax credit expensed or capitalized in the audited annual financial statements.
How should timing differences between books and GSTR-3B be reported?
Timing differences arising from invoices booked in one financial year but claimed in GSTR-3B of the subsequent financial year are reported in Table 12B and Table 12C of Form GSTR-9C.
What constitutes valid grounds for unreconciled ITC differences in Table 13?
Valid grounds include expenses where credit is ineligible under Section 17(5), permanent book adjustments, timing lags under Section 16(4), and reversal of credit due to non-payment to suppliers within 180 days.
Check your own GSTR-2B
Verify your purchase register against GSTR-2B data locally in your browser before filing annual returns and reconciliation statements. Your GSTR-2B and purchase register files are read in your browser and never uploaded to any server.
Last checked: 20 October 2026. Sources: Central Board of Indirect Taxes and Customs, GST Council Portal.