The coastal police said they had registered the case against the vessel after recording the statements of the fishermen, who were on board the fishing boat.
The boat was hit by the cargo vessel, about 40 nautical miles from Kollam, in international waters.
In their statement, the fishermen said the ship, which they could not identify, had gone southwards after the incident.
The crew of the ship had been charged under IPC sections 280 (rash navigation of vessel) and 337 (causing hurt by act endangering life or personal safety of others), the Kochi Coastal Police said.
The Navy had said the ship was "most likely" a Hong Kong-registered vessel and it would be asked to berth at a nearby Indian port for further investigations.
The ship is now in international waters.
"The ship involved has been identified most likely to be Ksl Ang Yang, registered at Hong Kong, and it is heading southwards," a Navy spokesperson had said yesterday.
The boat involved in the incident has also been brought to the Neendakara fishing harbour in Kollam district.
Kerala had also witnessed another fatal incident involving a foreign ship in February, 2012 when two fishermen from the state were shot dead by two Italian marines on board an oil tanker.
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