You filed your GSTR-1 on the 11th of the month, but when you open Table 3.1 of GSTR-3B, the numbers do not match your outward sales summary. In some cases, figures entered before filing GSTR-1 fail to refresh. In other situations, heavy sales returns produce an unexpected zero instead of reflecting your actual credit notes.
Why auto-populated liability differs from GSTR-1
The system computes outward tax liability in GSTR-3B Table 3.1 based on records submitted in Form GSTR-1 and optional Form GSTR-1A. Per GSTN GSTR-3B Portal Guidelines, discrepancies occur due to specific structural rules:
- Data saved prior to GSTR-1 filing: If a taxpayer opens and saves data in GSTR-3B before completing their GSTR-1 filing, the system does not overwrite the pre-existing draft values in Tables 3.1(a), (b), (c), (e), and 3.2. Downloading the system-generated GSTR-3B PDF displays the correct figures, while the screen draft retains stale entries. Re-generating the summary refreshes the numbers.
- Credit notes exceeding outward supplies: In GSTR-3B Table 3.1(a), negative tax values from GSTR-1 or GSTR-1A are not permitted. If downward amendments and credit notes exceed total outward taxable supplies for the period, the portal auto-populates zero. The unabsorbed credit balance cannot be offset as negative outward tax on that screen.
- GSTR-1A amendments: Taxpayers who furnish amendments or additions in Form GSTR-1A under Rule 59(4A) of the CGST Rules will see Table 3.1 update to reflect the net combined position of GSTR-1 plus GSTR-1A. If the GSTR-1A draft is left unfiled, Table 3.1 reflects only the original GSTR-1.
- Negative reverse charge in Table 3.1(d): When credit adjustments on inward supplies liable to reverse charge turn negative, the portal populates zero in Table 3.1(d).
Auto-population lock in Table 3.1: Per GSTN advisory on GSTR-3B auto-population, starting from the July 2025 tax period onward, outward liability auto-populated in GSTR-3B from GSTR-1, GSTR-1A, or IFF is non-editable. You cannot type over Table 3.1 directly on the screen. Any correction to outward liability must be made by filing Form GSTR-1A before submitting GSTR-3B for that period.
Rule 88C and DRC-01B implications
Discrepancies between outward liability declared and tax paid trigger automated compliance checks. Under Rule 88C of the CGST Rules, where the tax payable declared in Form GSTR-1 (as amended in GSTR-1A) exceeds the tax payable paid in Form GSTR-3B by the notified percentage and amount, Part A of Form GST DRC-01B is generated automatically.
If you receive a DRC-01B intimation, you must either pay the differential amount with applicable interest or file an explanation in Part B within the prescribed timeline. Under Rule 59(6) of the CGST Rules, failing to reply or pay blocks the filing of Form GSTR-1 for subsequent tax periods.
To understand the complete monthly mechanism, read our detailed guide on GSTR-3B format and how GSTR-2B feeds it.
Worked example: credit note impact on Table 3.1
Consider an enterprise, M/s Surya Trading, with the following outward supplies and credit notes during a tax period:
- Taxable outward supplies (B2B invoices): ₹2,00,000 (IGST @ 18% = ₹36,000)
- Credit notes issued for returned goods: ₹2,50,000 (IGST @ 18% = ₹45,000)
| Document Type | Taxable Value (₹) | IGST Liability (₹) | Portal Treatment in Table 3.1(a) |
|---|---|---|---|
| B2B Taxable Invoices | 2,00,000 | 36,000 | Taxable sales base |
| Credit Notes Issued | 2,50,000 | 45,000 | Deducted from sales base |
| Net Math (Sales - Credit Notes) | -50,000 | -9,000 | Negative net result |
| Auto-populated in Table 3.1(a) | 0 | 0 | Auto-populated as zero |
Mathematical check: Outward tax (₹36,000) minus credit note tax (₹45,000) equals -₹9,000. Because the portal rule does not permit negative liability in Table 3.1(a), the portal shows ₹0. Surya Trading cannot claim a cash refund or negative offset through Table 3.1(a) for this period. The remaining credit balance of ₹9,000 must be adjusted against outward liability in subsequent months.
Offsetting tax and handling payment in Table 6.1
Once Table 3.1 is verified, tax payment occurs in Table 6.1. Under GSTN Table 6.1 Payment of Tax Rules, tax liability offset can be done only once per tax period and cannot be executed in parts. Reverse-charge liability must be discharged strictly in cash (or against an available reverse-charge negative balance in the electronic cash ledger) and cannot be offset using input tax credit.
Frequently asked questions
Why is Table 3.1 in GSTR-3B showing zero when my credit notes exceed sales?
The GST portal does not allow negative outward tax liability in Table 3.1(a). If credit notes and downward amendments declared in GSTR-1 exceed outward taxable supplies for the month, the auto-populated field displays zero instead of a negative figure.
Can I manually change the auto-populated liability in GSTR-3B?
From the July 2025 tax period onward, outward liability auto-populated in GSTR-3B from GSTR-1 or GSTR-1A is non-editable on the GST portal. Any correction must be filed through Form GSTR-1A before filing GSTR-3B for that tax period.
What happens if GSTR-1 liability exceeds GSTR-3B tax paid?
Under Rule 88C of the CGST Rules, if tax payable in GSTR-1 or GSTR-1A exceeds the tax paid in GSTR-3B beyond the prescribed threshold, the portal issues Form GST DRC-01B Part A. The taxpayer must pay the differential tax with interest or explain the reasons within the specified time, failing which subsequent GSTR-1 filing is blocked under Rule 59(6).
Check your purchase register against GSTR-2B
While outward liabilities stem from GSTR-1, your inward tax credits in Table 4 depend on accurate GSTR-2B reconciliation. Match your purchase register against GSTR-2B in seconds. Your GSTR-2B and purchase register files are read in your browser and never uploaded to any server.
Last checked: 24 October 2026. Sources: CBIC CGST Rule 88C, GSTN GSTR-3B User Manual, GSTN Advisory on GSTR-3B Auto-Population.