Currently, traders can pay fees only manually or through net banking.
"The technical process to allow and enable payment of fee through debit/credit cards has been completed. The new Commerce Secretary Rita Teotia will formally launch the facility this week," an official said.
The Directorate General of Foreign Trade (DGFT) receives lakhs of applications every month and the fees ranges between Rs 100 to Rs 10,000.
The traders can avail this facility from all the public and private sector banks.
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Further efforts are also underway for message exchange and integration of DGFT's system with income tax department and Ministry of Corporate Affair for verification of PAN and DIN/CIN details respectively.
Once implemented, this would further reduce the processing time of applications at regional authority level.
The ministry is also engaged with different departments, including revenue and shipping, to reduce paper work in a bid to cut transaction cost for exporters and improve ease of doing business.
The government is aiming to improve India's overall ranking in ease of doing business index to 50th position in the next two years from the current 142nd.