How to Pay GST Online: PMT-06 Challan, CPIN, Payment Modes and Fixes When the Money Doesn’t Reflect

A Jaipur trader paid ₹86,400 through his bank app, saw the money leave his account, and assumed his GST was paid — then got a late-fee notice. His money had reached the government, but it was sitting in his electronic cash ledger while his GSTR-3B remained unfiled, and an unfiled return still draws late fee and interest. His mistake is the single most common GST payment misunderstanding in India: depositing money and discharging a liability are two different steps, and this guide keeps them separate.

For the wider GST picture, see the complete GST compliance guides on the GST hub. Once the money is in your ledger, how to file GST returns online after paying walks through the return itself, and if you are already late, exactly what late filing of GSTR-3B costs works out the damage by delay. Every November date, including GSTR-1 on 11 November and GSTR-3B on 20 November, sits in November 2026’s full tax due-date calendar, and the GSTR-1 filing guide and due-date tables cover the outward-supplies return that precedes payment. If interest is part of what you owe, work out interest on delayed GST with the GST interest calculator before you generate the challan.

Step 1: Generate the PMT-06 challan

Log in to gst.gov.in and go to Services → Payments → Create Challan. A challan can also be created before login using the GSTIN, which is useful when your accountant generates it and you pay it. Enter the amounts head by head: IGST, CGST, SGST/UTGST and cess as the major heads, and within each, tax, interest, penalty, fee or other amount as the minor heads. This split is the part that has to be right. Money paid into the CGST head cannot be used to pay an SGST liability. It is not lost — Form GST PMT-09 allows a transfer between heads within the same GSTIN — but a transfer is slow, and it will not save a due date.

Choose the payment mode, then generate the challan. The portal issues a CPIN — the Common Portal Identification Number, 14 digits — which identifies the challan and is normally valid for 15 days. If the challan expires before you pay, do not reuse it: generate a fresh one. Keep the challan; the CPIN is your reference if anything goes wrong.

Step 2: Pay, and know what each mode does

For NEFT/RTGS, the trap is the beneficiary: use exactly the account number and IFSC printed on the mandate form, and add the beneficiary well before the due date — some banks hold a new beneficiary for hours. For over-the-counter payments, the ₹10,000 per challan per tax period limit means a large liability cannot be split across counter challans; use an electronic mode instead.

Step 3: Confirm the CIN and the ledger credit

After a successful payment, the bank generates a CIN — the Challan Identification Number. The CPIN identifies the challan before payment; the CIN proves the money reached the government. Check Services → Ledgers → Electronic Cash Ledger (Form GST PMT-05) and confirm the GSTIN, head and amount. If the credit is missing, track it by CPIN or CIN under Services → Payments → Track Payment Status — most “missing” payments are NEFT transfers still in transit or credits under a wrong head.

Step 4: Discharge the liability in GSTR-3B

Here’s the catch from the Jaipur trader’s story. The cash ledger is a wallet, not a return. In GSTR-3B you set off the liability first against eligible input tax credit and then against the cash balance, and only then file. Interest, penalty and late fee can only ever be paid in cash, never from credit — so if your liability is mostly interest, the cash challan has to cover it in full. Filing a nil return, where there genuinely is nothing to pay, is a separate route and needs no challan at all.

Worked example: a Delhi supplier’s October GSTR-3B shows ₹1,20,000 of output tax, ₹75,000 of eligible ITC, and ₹4,500 of interest. The ITC absorbs ₹75,000, leaving ₹45,000 of tax plus ₹4,500 of interest — ₹49,500 — to be deposited by PMT-06 before filing. A challan for the full ₹1,20,000 would park ₹70,500 needlessly; one for only ₹45,000 would leave the return short by the interest and block filing.

When payment goes wrong

• Money debited, no CIN, no ledger credit. Wait for the bank’s reconciliation cycle, then track by CPIN. If the debit is genuine and the challan still shows unpaid after two working days, raise it with the bank with the CPIN and debit proof — and do not pay a second challan for the same liability until the first is resolved, or you will be chasing a refund.
• Paid under the wrong head. File Form GST PMT-09 to move the amount between major or minor heads within the same GSTIN. It fixes the ledger, but it takes time — which is why head accuracy at challan stage matters more than the fix.
• Challan expired. Generate a new PMT-06. An expired CPIN cannot be revived or paid.
• Paid after the due date. Interest runs from the day after the due date, and late fee accrues per day of delay. Pay tax, interest and late fee together, then file.
• Wrong GSTIN on the challan. This is the one error with no quick fix: money credited to another GSTIN’s ledger cannot be moved by PMT-09. Check the GSTIN character by character before generating the challan.

FAQs

What is the difference between CPIN and CIN?
CPIN is the 14-digit number the portal issues when the challan is generated, valid for 15 days. CIN is issued by the bank after successful payment and proves the money reached the government.

Can I pay GST without logging in?
Yes, a challan can be created pre-login using the GSTIN, and then paid through the available modes. The ledger credit still lands in that GSTIN’s cash ledger.

Does paying the challan mean my return is filed?
No. The challan only deposits money in the electronic cash ledger. You must still file GSTR-3B, setting off ITC and cash against the liability.

Can late fee and interest be paid from input tax credit?
No. Interest, penalty and late fee can only be paid in cash. Only the tax portion can be set off against ITC.

What if my payment is not reflecting in the ledger?
Track it by CPIN or CIN under Services → Payments → Track Payment Status. NEFT/RTGS credits can take until the next working day; if it is still missing after two working days, take the CPIN and bank debit proof to your bank.

Sources

Section 49 of the CGST Act, 2017 and Rule 87 of the CGST Rules, 2017 (Central Board of Indirect Taxes and Customs) — payment of tax, interest, penalty and other amounts through the electronic cash ledger, with the challan generated in Form GST PMT-06 and the ledger maintained in Form GST PMT-05; CPIN validity of 15 days and CIN issuance on successful payment are as prescribed in the GST portal’s payment process under Rule 87. Over-the-counter limit of ₹10,000 per challan per tax period and Form GST PMT-09 head-transfer facility are as provided in the CGST Rules payment framework. GSTR-3B monthly due date of the 20th of the following month is the standard return calendar applied in the November 2026 due-date schedule.