'M V Izumo', carrying soyabeans, was on its way to Singapore from Kandla yesterday when it allegedly hit the boat which sank, the sources said.
Three fishermen on the boat, 'Al Ameen', had jumped overboard just before the collision and were rescued by other fishing boats in the vicinity.
The CG sources said they were investigating the alleged involvement of the cargo vessel in the incident. Police and Mercantile Marine Department will carry out the probe, they said.
The incident occurred at about 3.45 PM yesterday about 18 nautical miles off Beypore.
The three fishermen have been admitted to a hospital in Cheruvannur in Kozhikode.
The sources said on receiving information about the incident, two fast-patrol vessels and a Dornier aircraft had been rushed to the area to locate the suspect vessel.
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Using state-of-the-art remote operating station at CG Headquarters at nearby Fort Kochi, two suspect vessels were identified. Inputs from the Maritime Rescue Coordination Centre (MRCC-MB) were also utilised in tracking the vessels.
The whole incident was reconstructed and the suspect vessel was identified as the Panamanian ship, the sources said.
Coordinated sea-air search operations and support from Cochin Port Trust resulted in identifying and subsequent interception of the suspect vessel within hours of the incident, a release said.
CG officials boarded Izumo and investigated navigational records, it said.
The photograph of the vessel and identification marks as revealed by the fishermen also matched with that of the intercepted vessel, CG sources claimed.
The incident comes hardly a year after two marines on board an Italian vessel 'Enrica Lexie' shot dead two Indian fishermen off Alappuzha coast mistaking them for pirates.