Four fishermen were reportedly missing after the ship collided with the boat which is named Don I.
The Coast Guard, marine enforcement and the Navy launched a rescue operation. Two helicopters of the Coast Guard are searching for the ship.
Four ships and a Dornier aircraft have been deployed to trace the ship that was involved in the incident.
Meanwhile, a case has been registered against and unknown vessel on two charges - IPC 280 for negligent navigation of vessel and IPC 340 for culpable homicide not amounting to murder.
The Union Home Ministry has also ordered an investigation into the incident.