The ship has been detained after two of its crew killed two Indian fishermen in February.
Notice has also been issued to the central government and one Goramma, the widow of one of the two fishermen who were killed by the Italian Marines on board the ship.
The apex court bench headed by Justice RM Lodha issued notice after senior counsel KK Venugopal said the two Italian Marines were already in police custody and their firearms had been seized.
The senior counsel told the court that the ship had nothing to do with the offence and in no way formed the property of the case.
The petition by the ship MT Enrica Lexie has challenged the Kerala High Court order detaining the Italian ship by staying the single judge order that permitted the ship to go.
The apex court was told that a 100,000 tonne ship has incurred a loss of Rs 200 crore ever since it was detained at the Kochi port and its losses were adding up every day.
The two Indian fishermen were allegedly mistaken as pirates and shot dead by the marines aboard Enrica Lexie Feb 15 off the coast of Alappuzha, Kerala.