Inquiry officers inspected the Panama-registered cargo ship 'Amber L', suspected to be involved in the incident.
The officers took the documents into custody in the presence of officials including those from coastal police, Indian coast guard and lawyers representing the owners of the vessel, the Mercantile Marine Department said in a statement here.
Customs, Immigration and Cochin Port Trust officials were also present during the inspection.
The Court had yesterday directed the two agencies to take safe custody of the original official log book, voyage data recorder, original log abstract, night order book and bell book, original GPS log and navigation chart for voyage of the vessel 'Amber L', suspected to be involved in the incident.
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Justice P B Suresh Kumar had passed the order on a petition by a co-owner of the boat who apprehended that digital records of the ship could be destroyed if they were not impounded.
Out of the 14 crew members on-board, 11 were rescued by fishing boats operating in the vicinity and two bodies were recovered.
One fisherman Motidas from Assam is missing after the collision.
Coastal police authorities said a coordinated search and rescue operation by the Indian Navy and the Indian Coast Guard is on to locate the missing fisherman.
The ship along with its crew was detained soon after the incident.