Invoice number, GSTIN and date all agree, yet the tax is not the same in your register and in GSTR-2B. This page finds the cause and decides what to claim. A gap of a rupee or two is usually rounding (its own guide), and the total gap between books and statement is in the 2B-versus-register bridge.
How the tool decides that tax does not match
What the tool compares decides what it can see. This is what it does today.
- Total tax per invoice. For GSTR-2B it adds integrated tax, central tax, State/UT tax and cess. For your register it uses the tax column you pick in the mapping step; if you pick none, it adds the columns whose headings contain IGST, CGST, SGST or cess.
- Each tax head separately. The tool also keeps IGST, CGST, SGST and cess apart for each invoice. In GSTR-2B they come from the tax columns. In your register it looks for columns named IGST (or Integrated tax), CGST (or Central tax), SGST, UTGST (or State/UT tax) and Cess, and it uses them only when they add up to the invoice’s tax figure within ₹1.00. A register with only one tax total column (a “Tax Amount” column, for example) is compared on the total alone.
- Tolerance of ₹1.00, per head. The total and each head are compared with the same ₹1.00 tolerance, and the tolerance is fixed. If all of them are within ₹1.00, the invoice is Matched (bucket A). If the total differs by more than ₹1.00, it goes to Value mismatch (bucket B) with the note “Tax amount mismatch” and the difference. If the total agrees but one head differs by more than ₹1.00, it also goes to Value mismatch, with the note “Tax head mismatch (IGST vs CGST+SGST)” when tax sits under IGST in one file and CGST plus SGST in the other, or “Tax head mismatch” followed by the heads that differ, such as CGST and SGST, in other cases. The difference shown is the difference in total tax, so it is 0.00 for a pure head swap.
- Not compared: the taxable value.
- Several rows for one invoice. In a GSTR-2B Excel file, rows with the same GSTIN and invoice number are added together. In your register, a second row with the same GSTIN and number goes to “Duplicates in books” and is not added.
- Partial ITC. If the GSTR-2B JSON carries a partial-ITC percentage for an invoice, the tool applies it to the 2B tax and notes “Partial ITC” with the percentage.
The causes, in the order to check them
| Cause | What the numbers look like | Who fixes it |
|---|---|---|
| 1. Rate or taxable value differs | The difference divided by the taxable value is a clean percentage | Whichever side is wrong |
| 2. IGST versus CGST plus SGST | The total is the same but the heads differ; the tool shows Value mismatch with “Tax head mismatch (IGST vs CGST+SGST)” when your register has head columns | Whichever side is wrong |
| 3. Round-off | A few paise to a rupee or two | Nobody; follow your round-off policy |
| 4. Invoice booked in parts | Your tax is a fraction of the 2B tax, and the same number sits in Duplicates in books | You |
| 5. Wrong tax head or column | The difference equals one head, such as cess, or a reverse-charge amount | You, by correcting the mapping or the entry |
1. The rate or the taxable value differs
Divide the difference by the taxable value. If it comes out as a clean percentage, say 6%, the two sides used different rates on the same value. If the 2B tax is lower in the same proportion as the taxable value, the supplier reduced the value, for example by an amendment in the B2BA table. We do not state rates here: which rate applies to a supply is a question for the supplier and your CA. A supplier can amend a current-period record through GSTR-1A after filing GSTR-1 and before filing GSTR-3B (GSTN GSTR-1A FAQ); see amended invoices and GSTR-1A.
2. IGST versus CGST plus SGST
Sometimes your register shows CGST plus SGST where GSTR-2B shows IGST, or the other way round. The total is unchanged, but the tool compares each head, so the invoice goes to Value mismatch with the note “Tax head mismatch (IGST vs CGST+SGST)” and a difference of 0.00. This works when your register has IGST, CGST and SGST columns that add up to its tax figure. If your register has only a total tax column, the tool compares the total alone and cannot see the swap, so compare the heads yourself against the integrated, central and State/UT tax columns of the GSTR-2B file. Which pair is right depends on the place of supply, and we do not state those rules here; take the invoice to your CA. GSTN’s GSTR-3B guide does say that invoices on which ITC is not available because of Section 16(4) and because the place of supply is in the supplier’s State are auto-populated in Table 4(D)(2), so the portal treats place of supply as an ITC question.
3. Round-off
Tax payable is rounded off to the nearest rupee under Section 170 of the CGST Act: 50 paise or more is increased to one rupee, and less than 50 paise is ignored. Suppliers and ERPs round at different points, so a gap of a rupee or less is common and the tool treats it as Matched, provided the total and each head are within ₹1.00. A gap of ₹2 or ₹3 on the total is flagged, so look at the invoice before calling it rounding (round-off mismatch guide).
4. The invoice is booked in parts
This one is a data problem, not a tax problem. If your register carries one invoice as two rows, for example goods and freight on separate lines with the same invoice number, the tool counts the first row and moves the second to Duplicates in books. The mismatch it shows is then the tax on the second row. Merge the rows into one invoice before you load the file. Where goods against one invoice arrive in lots, credit may be taken on receipt of the last lot (Section 16(2), first proviso), so book the invoice once at full value and track receipt separately. For real duplicates, see duplicate invoices.
5. A wrong tax head or column
If the difference equals one head, the cause is probably in how your register is laid out. Cess is an example: the tool adds the cess column of GSTR-2B to the 2B tax, so a register whose “Tax” column holds only CGST plus SGST will be short by the cess amount. A reverse-charge invoice is another: your register may show nil tax while the 2B row carries an amount (RCM invoices in GSTR-2B). Fix the mapping or the entry. Whether cess credit is available on your goods is a separate question that this page does not answer.
How to find the cause in four steps
- Open Value mismatch and start with the largest Diff. The list shows Tax (2B), Tax (books) and Diff, and the Excel export adds Taxable (books) and a note, so you can sort it by Difference in Excel. The biggest differences carry the most ITC (how to find where your mismatches are).
- Divide Diff by the taxable value. A clean percentage points to cause 1.
- Check Duplicates in books for the same invoice number. If it is there, you have cause 4.
- Read the notes for Partial ITC, Amended and Reverse Charge, then look for “Tax head mismatch”, which means the total agrees but the tax sits under a different head. If your register has only a total tax column, check the heads in the GSTR-2B file yourself, because the tool then compares the total alone.
What to claim while the difference is open
ITC is available only on details communicated in GSTR-2B (Section 16(2)(aa); Rule 36(4) from 1 January 2022), and input tax means the tax charged on the supply, which is on the invoice you hold (Section 2(62); Section 16(2)(a)). So you cannot claim more than the 2B figure, or more than the invoice charges. Our working rule, which is practice and not law, is to claim the lower of the two and carry the rest. Claiming a higher books figure risks a DRC-01C intimation once the gap crosses the pre-defined limit (how to reply to DRC-01C), and interest at 18% a year applies to ITC wrongly availed and utilised.
The tool’s supplier email lists each mismatched invoice with both amounts. A message of your own can say the same:
Worked example: five invoices, one real recovery
A distributor’s September 2026 register is loaded against GSTR-2B, and five invoices show some tax difference. (Rates are illustrative. The register has separate IGST, CGST and SGST columns, so the tool compares heads as well as totals.)
| Invoice | Tax in books | Tax in 2B | What the tool shows | Cause | Claim now |
|---|---|---|---|---|---|
| INV-2041 | ₹36,000 | ₹24,000 | Mismatch, ₹12,000 | Invoice at 18%, supplier reported 12% on the same ₹2,00,000 | ₹24,000 |
| INV-5530 | ₹18,000 (two rows) | ₹18,000 | Mismatch, ₹7,200; second row in Duplicates | Booked in two rows, ₹10,800 and ₹7,200 | ₹18,000 |
| INV-9077 | ₹27,000 | ₹22,500 | Mismatch, ₹4,500 | Supplier amended the taxable value from ₹1,50,000 to ₹1,25,000 | ₹22,500 |
| INV-0612 | ₹7,082.40 | ₹7,082.00 | Matched | Round-off, ₹0.40 | ₹7,082 |
| INV-318 | ₹18,000 (CGST ₹9,000 + SGST ₹9,000) | ₹18,000 (IGST) | Mismatch, ₹0.00: “Tax head mismatch (IGST vs CGST+SGST)” | Head differs; totals agree, so only the head check catches it | ₹18,000, after the head is confirmed |
| Total | ₹1,06,082.40 | ₹89,582.00 | ₹89,582 |
Check the totals. Books: ₹36,000 + ₹18,000 + ₹27,000 + ₹7,082.40 + ₹18,000 = ₹1,06,082.40. GSTR-2B: ₹24,000 + ₹18,000 + ₹22,500 + ₹7,082 + ₹18,000 = ₹89,582. The gap is ₹1,06,082.40 − ₹89,582 = ₹16,500.40.
The tool flagged ₹12,000 + ₹7,200 + ₹4,500 = ₹23,700. Of that, ₹7,200 is not real: once the two INV-5530 rows are merged, books and 2B agree. INV-318 is also in Value mismatch, but with a difference of ₹0.00 and no money at stake once the head is confirmed. The real gap is ₹12,000 + ₹4,500 + ₹0.40 = ₹16,500.40, and only part of it can be recovered. The ₹12,000 on INV-2041 comes back if the supplier amends its return, so it is worth a message. The ₹4,500 on INV-9077 does not, because the supplier reduced the value, and the books must come down to ₹22,500. The ₹0.40 is round-off. Had the firm claimed its books figure, it would have been ₹16,500.40 above GSTR-2B.
If the invoice is missing, not wrong, go to invoices in books but not in GSTR-2B. For every error type in one table, start from common GSTR-2B reconciliation errors and fixes.
Frequently asked questions
What tax difference does the tool treat as a match?
The tool compares the total tax of each invoice and each tax head (IGST, CGST, SGST and cess) with a tolerance of ₹1.00. If the total and every head are within ₹1.00, the invoice is matched. A difference above ₹1.00 on the total or on any head goes to the Value mismatch list, with the difference in total tax shown.
Why does GSTR-2B show a different tax amount from my invoice?
The usual causes are a different rate or taxable value, an IGST versus CGST plus SGST split, round-off, an invoice booked in parts in your register, or a head such as cess that is missing from your tax column. Divide the difference by the taxable value to see whether it is a rate gap.
GSTR-2B shows IGST but my books show CGST and SGST. Will the tool flag it?
Yes, if your register has IGST, CGST and SGST columns that add up to its tax figure. The tool then puts the invoice in Value mismatch with the reason “Tax head mismatch (IGST vs CGST+SGST)”, even though the total agrees. If your register has only a total tax column, the tool compares the total alone, so check the heads in the GSTR-2B file yourself. Ask the supplier to confirm the place of supply.
Which amount should I claim when my books and GSTR-2B differ?
ITC is limited to what GSTR-2B communicates and to the tax charged on the invoice you hold. Until the difference is explained, claim the lower of the two and carry the rest. This is a working practice, not a legal rule.
Why is one invoice in Value mismatch and again in Duplicates in books?
Your register probably carries the invoice as two rows with the same number. The tool uses the first row and moves the second to Duplicates in books, so the mismatch equals the second row. Merge the rows and run it again.
Is a ₹2 round-off difference a mismatch?
In the tool, yes, because it is above ₹1.00. Check the invoice, then follow your round-off policy. Section 170 of the CGST Act rounds tax payable to the nearest rupee, and suppliers and ERPs can round at different points.
Find your tax mismatches in minutes
Add your GSTR-2B and purchase register and the tool lists every invoice whose total tax, or any tax head (IGST, CGST, SGST, cess), differs by more than ₹1.00 in the Value mismatch list, with the tax in 2B, the tax in your books and the difference, plus a supplier email you can copy. If your register has only a total tax column, it compares the total alone. Your GSTR-2B and purchase register files are read in your browser and never uploaded to any server.
Last checked: 1 Oct 2026. Sources: Notification 39/2021-Central Tax (Section 16(2)(aa)), Notification 40/2021-Central Tax (Rule 36(4)), Section 16, CGST Act, Section 2, CGST Act, Section 170, CGST Act, GSTN GSTR-1A FAQ, GSTN GSTR-3B user guide, GSTN FAQ on GSTR-2B tables, GSTN advisory on DRC-01C, Notification 13/2017-Central Tax (interest rate).