The naval guards-- Latore Massimiliano and Salvatore Girone-- were arrested by the Kerala police on February 19 and brought to the land from the ship which was intercepted and wharfed at Kochi Port.
They have been charged with murder under section 302 of the Indian Penel Code.
The deceased - Valentine Jalastine and Ajeesh Binki - last week had set out to sea in a boat along with nine fellow-fishermen from Neendakara fishing harbour.
They were allegedly killed by the marines of the ship who fired at their boat on February 15.
The Italian authorities have contended that the fishing boat was fired at because it was mistaken to be a pirates' vessel.
After four days of negotiations involving Indian and Italian diplomats, the Naval guards were arrested by police in Kochi.
They were later questioned by a team of senior police officials including Kochi City Police Commissioner MR Ajith Kumar and Kollam SP Sam Christy Daniel.
Meanwhile, Cochin Port sources said the Italian vessel would be moved to the outer anchorage within the port limits.
The ship is presently inside the oil terminal due to which other oil tankers of various companies are finding it difficult to discharge cargo.
Two tankers of Kochi Refinery are in the outer harbour waiting to discharge their cargo containing furnace oil, Euro-III and Euro-IV products.
Cochin Port and Coastguard would monitor the movement of the Italian ship, Port sources said.