The Press Trust of India news agency said the National Investigation Agency also filed cases under maritime laws which carry a maximum penalty of death.
A major diplomatic row broke out between India and Italy last month when Rome said the marines would not return to India after they were allowed to go home to vote in an election.
The marines eventually returned after India gave an assurance that they would not face the death penalty if convicted.
India's Supreme Court ruled earlier this year that the men should be tried by a special court to be set up by the central government. The decision removed the case from the jurisdiction of the southern state of Kerala, near where the shooting took place.
India's home ministry has directed the agency to investigate all aspects of the case and present it to the special court that will be appointed by the Indian government.
Minister of External Affairs Salman Khurshid met Friday with Italian Deputy Foreign Minister Staffan de Mistura and briefed him about the procedure that the special court will follow in dealing with the marines, ministry spokesman Syed Akbaruddin said.
Khurshid later spoke over the phone with Italian Prime Minister Mario Monti.
Khurshid assured de Mistura last month that the death penalty in India applies only in the "rarest of rare" cases, and that the marines' case did not fall into that category.
The marines, Massimilian Latorre and Salvatore Girone, were part of a military security team on a cargo ship when they fired at the fishermen, mistaking them for pirates.
Italy maintains that the shooting occurred in international waters and that Rome should have jurisdiction. India says the ship was in Indian territorial waters.