The elite agency was handed over the case earlier this month. It was earlier being handled by the Kerala Police. The Supreme Court had said in January this year that the Kerala government did not have jurisdiction to investigate the case.
Italy has, however, objected to the government's decision that the case will be investigated by the NIA as the agency is empowered to deal with maritime piracy and terrorism, and serious charges can lead to a call for the death penalty.
The Centre has said that the two marines, Salvatore Girone and Massimiliano Latorre, who have been charged with murder, will be tried by a special court in Delhi with daily hearings. Kerala had sought that a special court be set up in their state to try the Italian marines, who returned to India to stand trial last month after days of Italy refusing to send them back.
They marines flew back to India in a dramatic turnaround on March 22, resolving a diplomatic crisis. India has agreed that if convicted, the marines can serve their sentence at home. India has also given Italy an assurance that the marines will not face the death penalty and that they would be housed at the Italian embassy in Delhi during their trial.
The marines had been allowed in February to travel home for four weeks by the Supreme Court to vote in the national elections after the Italian ambassador Daniele Mancini gave a written assurance that they would return to face trial in India. When Rome said it was reneging on its commitment, the Supreme Court had banned Mr Mancini from leaving India; Italy had then protested that it violated diplomatic immunity.
The naval officers were guarding an Italian tanker when they say they mistook the fishermen for pirates and opened fire. Italy says the shooting took place in international waters and India has no jurisdiction. New Delhi disagrees.