Custom duty is a tax levied on Goods imported into India Whether you are an importer, freight forwarder, or logistics professional, this is very important for you to know how to pay customs duty online, efficiently and accurately which can save your time, money and compliance.
In this comprehensive guide, we break down:
- What customs duty is
- How to calculate it
- Step-by-step payment process via ICEGATE
- Common mistakes to avoid
- How automation with SEPFUST BOE Reader & Customs Data Automation can help
👉 Start here: Visit the SEPFUST Home Page to explore all trade automation solutions.
What is Customs Duty?
It is a tax which is imposed on goods imported into a country. In India, this duty is determined by:
✔ Classification under the Customs Tariff Act
✔ Assessable value of imported goods
✔ Applicable exemptions or notifications
This duty is required to be paid before goods are cleared through customs and delivered.
Why Paying Customs Duty Online Matters
Gone are the days of manual challans and bank counter payments. The Government of India has made online customs duty payment mandatory for most import transactions through ICEGATE
(Indian Customs Electronic Gateway).
Earlier manual challans and bank counter payments were used. But Government of India has made the online customs duty payment mandatory for most import transaction through ICEGATE(Indian Customs Electronic Gateway)
Benefits include:
- Instant payment confirmation
- Digital audit trail
- Faster customs clearance
- Reduced errors vs manual cash ledger entries
Step-by-Step: How to Pay Customs Duty Online
Here’s the exact sequence you should follow:
Step 1: Calculate Duty Payable
Before you make a payment, determine your duty liability using:
- The Bill of Entry filed on ICEGATE
- Details of value, quantity, duties (IGST, BCD, CVD), cess, etc.
- Duty calculation formulas and notifications
Tip: Validate values to avoid under/over payment.
Step 2: Generate Duty Payment Advice on ICEGATE
- Log in to ICEGATE with your credentials
- Navigate to e-Payments Dashboard
- Select “Duty Payment Advice”
- Enter:
- Bill of Entry number
- Importer details
- Duty components you intend to pay
- Generate ONLINE duty payment advice
This generates a Payment Advice Number (ICD/PORT/CHA)
Step 3: Make Payment Through Internet Banking / Debit / Credit Card
Once payment advice is generated:
- Choose preferred bank from ICEGATE-supported partner banks
- Pay via net banking / debit / credit cards
- Ensure the amount matches duty payable
- Complete 2FA authentication
After successful payment:
✔ e-receipt is auto-generated
✔ Debit entry is updated in customs ledger
✔ Customs releases the goods for clearance
Step 4: Download Payment Receipt and Proof
After payment:
- Download PDF receipt from ICEGATE
- Save it for:
- Customs audit
- Accounting
- GST reconciliation
- You may also need it for drawback claims or import notifications
Common Mistakes While Paying Customs Duty Online
There are so many data points which one needs to check, even seasoned professionals make these mistakes. You need to avoid following:
- Not reconciling BOE values before paying
- Paying incorrect duty components
- Using wrong Payment Advice number
- Not downloading the payment receipt
- Losing digital receipts
- Proper validation and automation can prevent these costly errors.
How SEPFUST Helps with Customs Duty & Compliance
In India exports is still a process in which a lot of manual paper work is required, people often do not fall because of legal obligation they fall because of the data mismanagement. Automating customs documentation not only speeds up processing, it increases accuracy dramatically.
SEPFUST Bill of Entry (BOE) Reader
Instead of copying BOE data manually:
✔ Extract BOE fields automatically
✔ Centralize duty components
✔ Prepare duty calculation sheets
✔ Save to Excel/ERP
Automated BOE extraction reduces human error and speeds up duty preparation.
Try the SEPFUST BOE Reader now (link to your BOE reader tool)
SEPFUST Customs Automation Suite
Beyond BOE:
- Extract invoices, packing lists, GRs, shipping bills
Create structured data for:
- GST reconciliation
- Duty drawback claims
- Audit trails
- Bulk processing for high-volume importers
FAQs: Paying Customs Duty Online
1. Can I pay customs duty without ICEGATE?
No. Most duty payments must be routed through ICEGATE’s e-payments portal for clearance.
2. What payment modes are accepted?
Net banking, debit cards, credit cards, UPI (if supported). Confirm with your bank list on ICEGATE.
3. Can I correct duty after payment?
Adjustments may be possible via rectification, but always validate before paying.
4. How does BOE data impact duty payment?
The duty amount calculated depends entirely on the Bill of Entry values and classification — accuracy matters.
5. Does SEPFUST help with duty calculation?
SEPFUST extracts data that feeds your duty calculations, but you should validate with customs rules or a CCA.
Final Thoughts
Paying customs duty online should be:
- Fast
- Accurate
- Auditable
- Linked with your compliance workflows
Manual methods increase risk, automation through SEPFUST BOE Reader & Customs Suite ensures accuracy, compliance, and operational efficiency.
Ready to automate import document data extraction and duty workflows?
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SEPFUST automates customs and trade documentation by extracting structured data from BOEs, invoices, and shipping bills. Reduce errors, improve compliance, and accelerate import-export operations.
Rishi Raj
Rishi Raj is a marketing professional with strong domain expertise in Finance and Technology, bringing over 3+ years of experience in driving growth-led marketing initiatives. He has a proven track record in building scalable go-to-market strategies, demand generation, and positioning technology products for measurable business impact.