The ship, 'Amber L', which left the scene after the incident,was detained along with its crew after a massive searchby the Navy and Coast Guard, Inspector General of Police (Ernakulam Range) P Vijayan told PTI.
Additional Director General of Police Tomin J Thachenkary, who is also heading the Kerala Coastal Police, said the ship was subsequently taken into custody.
The authorities in Kerala are waiting for the Centre's nod to initiate legal action against the captain of the ship and others responsible for the accident.
Kerala Fisheries Minister J Mercykuttyamma said the captain and crew could be booked under the IPC provision dealing with culpable homicide.
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The injured fishermen were admitted to various hospitals here and the condition of two of them was stated to be serious, the police said.
Another occupant of the boat was missing and a search operation was on to rescue him.
The boat carrying 14 fishermen was hit by the ship at around 2 am, around 20 nautical miles off the Kochi coast. Most of the fishermen on board the boat were from Tamil Nadu and Assam, the police said.
The rescued fishermen said their boat was hit while it was being anchored in the sea after fishing.
A Cochin Port Trust official said the ship, which was taken into custody by the police, could not be berthed at the Port Trust due to its huge size.
The ship could remain in the outer anchorage position, he added.
The fishing vessel, named Carmel Matha and owned by Nazaer Palluruthy, capsized immediately after it was hit by the ship.
The Navy said a search-and-rescue operation was on and an advanced light helicopter and the INS Kalpeni were pressed into service to trace the missing fisherman.
In February 2012, two fishermen were shot dead allegedly by Italian marines on-board an oil tanker, Enrica Lexie.
Kerala Chief Minister Pinarayi Vijayan has announced an aid of Rs two lakh each for the families of the deceased fishermen.
It will be given from the Labour Department's Settlers Employees Welfare Scheme, he said in a statement in Thiruvananthapuram.
Usually, only those registered under the scheme are entitled to an aid. However, the government has decided to give a special relaxation in this case and directed the Labour Department to provide the aid, said Vijayan.
The Coastal Police and the Fisheries Department have been asked to remain vigilant as regards the safety of the fishermen who put out to sea.