GST Payment Online: Challan PMT-06, Ledger Use and Payment Process
Manish Sahu
GST Compliance & Accounting Specialist
GST payment online is the process of paying tax, interest, late fee, penalty or other permitted amounts through the official GST Portal. A taxpayer can create a payment challan, enter the applicable amounts and deposit money into the electronic cash ledger.
The amount credited to the electronic cash ledger can be used to pay tax, interest, late fee, penalty and other permitted liabilities. Eligible input tax credit in the electronic credit ledger may be used only for permitted tax payments and cannot normally be used for interest, late fee or penalty.
What is a GST payment challan?
A GST payment challan is an electronic document used to deposit money into the Government’s GST system. It records the taxpayer details, payment reason, amount under each tax head and selected payment method.
After the payment is successfully completed, the amount is credited to the electronic cash ledger linked with the GSTIN. The challan reference number and payment confirmation should be saved with the business records.
What is Form GST PMT-06?
Form GST PMT-06 is the challan used for depositing an amount into the electronic cash ledger. It can be generated through the GST Portal before completing the payment.
The taxpayer should enter the amount under the correct heads, such as IGST, CGST, SGST or UTGST. Separate amounts may also be entered for interest, late fee, penalty and other liabilities where applicable.
When is GST payment required?
A registered person may need to make payment for the following:
Output GST on taxable sales
Tax payable under reverse charge
Interest for delayed payment of tax
Late fee for delayed return filing
Penalty or other amounts payable under an order
Additional liability disclosed during return filing
For reverse-charge transactions, the recipient generally pays the applicable tax through the prescribed method before claiming eligible input tax credit. Read our Reverse Charge Mechanism under GST guide for related information.
How to make GST payment online
Visit the official GST Portal.
Go to Services, Payments and Create Challan.
Enter the GSTIN or other permitted identification details.
Enter the amount under the correct tax, interest, late fee, penalty or other payment heads.
Review the total challan amount carefully.
Select the available payment method.
Generate Form GST PMT-06.
Complete the payment through the selected banking or payment facility.
Save the CPIN, CIN, bank reference number and payment confirmation.
Check that the amount has been credited to the electronic cash ledger.
The GST Portal also allows challan generation through the pre-login facility. However, the taxpayer must carefully enter the GSTIN or other permitted identification details and verify the amount before proceeding.
GST payment methods
Depending on the facility available on the GST Portal, taxpayers may be able to pay through internet banking, debit card, credit card, UPI or other authorised payment methods. Over-the-counter payment and NEFT or RTGS facilities may also be available subject to the applicable limits and banking arrangements.
Transaction limits, bank charges and processing times can differ between payment methods. Keep the bank reference number and portal confirmation until the amount appears in the electronic cash ledger.
Before making GST payment online, check whether sufficient balance is already available in the electronic cash ledger. This helps prevent duplicate deposits and unnecessary blocking of business funds.
Electronic cash ledger and electronic credit ledger
The electronic cash ledger contains money deposited by the taxpayer or another permitted person on behalf of the taxpayer. It can be used for payment of tax, interest, late fee, penalty and other permitted liabilities.
The electronic credit ledger contains eligible input tax credit. Credit can be used only for permitted tax liabilities under the utilisation rules. It cannot normally be used to pay interest, late fee or penalty.
Before filing a return, compare the tax liability with both ledgers. Eligible credit may reduce the output tax payable, but the remaining tax and non-credit liabilities generally need to be paid through the cash ledger.
Example of GST payment calculation
Particular | Amount |
|---|---|
Output GST liability | ₹30,000 |
Eligible input tax credit | ₹18,000 |
Tax payable after eligible credit | ₹12,000 |
Late fee | ₹500 |
Total cash payment required | ₹12,500 |
This example is for explanation only. The actual amount may change because of tax type, credit utilisation rules, credit reversals, interest and the figures reported in the return.
GST payment while filing GSTR-3B
While preparing GSTR-3B, the taxpayer reports outward tax liability, reverse-charge liability, eligible input tax credit and other required details. The portal displays the amount payable based on the information entered.
The taxpayer can use eligible credit and the balance in the cash ledger to discharge the permitted liability. Interest, late fee and penalty generally require payment through the electronic cash ledger.
After payment and verification, the return can be filed using the permitted electronic verification method. For a detailed comparison of the two important returns, read our GSTR-1 and GSTR-3B guide.
How to check GST payment status
Log in to the GST Portal or open the payment service.
Go to the challan or payment history section.
Search using the CPIN, CIN or other available reference details.
Check whether the status is successful, failed, pending or expired.
Confirm that the amount is reflected in the electronic cash ledger.
If money is debited from the bank account but the challan is not updated, do not immediately make a second payment. First check the payment status, bank account and electronic cash ledger. If the issue continues, contact the bank or GST helpdesk with the transaction reference.
Common mistakes in GST payment
Selecting CGST instead of IGST or SGST
Entering the wrong amount under interest or late fee
Using an incorrect GSTIN
Paying without checking the available ledger balance
Claiming input tax credit for interest or late fee
Making a duplicate payment after a delayed status update
Failing to retain the challan and bank reference
Ignoring reverse-charge liability while preparing the return
GST payment and invoice records
Payment records should agree with the sales register, purchase register, tax invoices and GST returns. If your business prepares invoices using InvGear, keep the tax summary and payment confirmation together for monthly reconciliation.
You can also review our GST invoice format guide and Input Tax Credit under GST guide.
Conclusion
GST payment online is straightforward when the taxpayer first checks the liability, selects the correct tax heads and verifies the electronic ledgers. Generate Form GST PMT-06 through the official GST Portal, complete the payment, save the confirmation and reconcile the amount before filing the return.
Always follow the latest GST Portal instructions, applicable return rules and CBIC notifications because payment procedures, deadlines and available facilities may be updated.