The CPT said the incident occurred when the vessel was being towed into the harbour "unauthorisedly violating the International Ship and Port Facility Security (ISPS) Code by another fishing boat".
There were no personnel on board the boat that sank, the Port Trust said in a release.
The police said the fishing boat was towed to the shore after it developed a technical snag in the sea during fishing.
The hydrographic survey team of the Cochin Port is carrying out surveys in the area to locate the vessel and determine the safe depths in the channel, the official said.
"The position of the sunken vessel has been identified by the surveyors of the Cochin Port Trust," the Port Trust said.
The Navy has been informed about the incident as it is a key channel being used by the Southern Naval Command and Cochin Shipyard, they said.
"Once the location of the wreck is established the same will be marked with a buoy," the Port Trust said.
"No environmental hazard is noticed due to the incident," they said.
They said a case has been registered against the fishing vessel.
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