After hearing arguments, Judicial Magistrate C Kathiravan sent Lalit Kumar Gurung, Radhesh Dhar Dwivedi (both Indians) and U.K. National Paul Towers to police custody.
Police had sought seven days custody of the trio for further interrogation.
The ship and its 35 member crew have been detained here for the past two weeks for illegally carrying arms and ammunition.
The bail petitions of all the 35 crew members, filed before a sessions court here, is likely to come up for hearing tomorrow.
Police had arrested all the crew members, including 12 Indians, on board the ship off Tuticorin on the charge of unauthorisedly entering Indian waters and possessing arms and ammunitions without valid documents.