This, the Minister said, is in sync with Prime Minister Narendra Modi's Digital India drive.
Efforts are also on to convert some 1,300 islands and all light houses into tourist attractions in a bid to tap their vast untapped potential, Gadkari said while launching the online collection of dues.
"Till now, sailing ships were forced to make payments manually for navigational aids provided by light houses as per an outdated law of 1927, causing the ships to remain stranded for 2-3 days. Now, the online system will not only result in removing hardships faced by foreign flags, but result in ease of business as promised by the PM," Gadkari explained.
Terming it as "a major step" towards e-governance, Gadkari said the plan to convert light houses and 1,300 islands into tourist spots will lead to generation of huge revenue, thus bolstering economic growth.
He said islands will feature water sports, resorts, light-and-sound shows to bring in tourists.
The Minister added that 15 lighthouses, including Mahabalipuram, Chennai, Kanyakumari, Rameshwaram, Konark and Kanhoji Angre have been identified, and IL&FS has done the feasibility study.
Director General of Lighthouses & Lightships (DGLL) Captain AM Surej said online collection will avoid the delay caused by manual mode of payment and enable ship owners to secure prompt light dues clearances from the Customs and port authorities.