Currently, traders can pay fees only manually or through net banking.
"Efforts are underway to allow/enable payment of fee through debit/credit cards, which would further facilitate this process. Once implemented the online system would be made mandatory," an official statement said.
The ministry has also operationalised online filing of Importer Exporter Code (IEC) number applications and online processing and issue of e-IECs in digital format.
Now new entrepreneurs, exporters and importers can apply online for issue of new IEC online with no more visits to the Regional Authority`s office required and upload the documents and pay the required fee through net banking, it said.
"However, till such time payment through debit/credit cards is enabled, the existing offline/manual system has also been allowed side by side, in order to facilitate those applicants who do not have net banking facility," it said.
It said that 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 e-IEC applications at regional authority level (possibly one day only)," it added.
"This is an important and path breaking initiative by Department of Commerce/DGFT (directorate general of foreign trade) towards 'Digital India' vision of Prime Minister of India and 'Ease of Doing Business'," it said.
The ministry is 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.