The Mercantile Marine Department (MMD), Kochi, which conducted an inquiry into the incident, has ordered the detention of the ship, 'Amber L', at Kochi till further orders.
An "initial report" on the incident was submitted to the Directorate General of Shipping yesterday, the MMD said.
A copy of the report was provided to the other agencies concerned, including the Kerala police.
The MMD said that based on digital and physical evidence, it had prima facie concluded that "the Panama Flag Bulk Carrier, Amber L, IMO No. 9200354, is the merchant ship involved in the collision with the Indian fishing boat, Carmel Matha, at about 0223 hours on June 11 off the Kerala coast".
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The causes and circumstances of the incident, along with the contributing factors, violations of national or international maritime laws, if any, professional lapses and human errors would be included in the "final report", to be submitted to the Centre, it added.
The final report will also have details, including the extent of involvement of both the vessels in the incident and the recommendations to "avoid recurrence of such unfortunate incidents in the future".
Of the 14 crew members on board the fishing boat, 11 were rescued by other such vessels in the vicinity and two bodies were recovered, while one fisherman, Motidas from Assam, was missing.