Chief Minister K Palaniswami said the victim J Antony John hailed from Colachel in Kanniyakumari in the state and expressed grief over his death.
"I express my deepest condolences and sympathies to the family of John, who hails from Tamil Nadu. I have directed that a sum of Rs two lakh be paid to his family from the Chief Minister's Public Relief Fund," he said in a statement.
Of the 14 crew members on-board, 11 were rescued by fishing boats operating in the vicinity and two bodies were recovered. One fisherman is missing after the collision.
The merchant ship has been directed not to leave Kochi till the investigation process is complete.