The court directed the master of the vessel, Amber L, to keep the ship in Indian territorial waters.
Justice P B Suresh Kumar also directed the central government to ensure that the vessel remains anchored in Indian territorial waters.
The order was issued on a petition filed by the victims of the accident.
Earlier, the coastal police had arrested the captain and two crew members of the merchant ship.
The Mercantile Marine Department (MMD), Kochi, which conducted an inquiry into the collision that took place off the coast here, had ordered the detention of the ship at Kochi till further orders.
Two fishermen were killed and 11 others injured when the merchant ship hit their fishing boat.
Of the 14 crew members on board, 11 were rescued by other such vessels in the vicinity and two bodies were recovered.
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