The death toll from a boat accident off an Indonesian island rose to 54 on the third day of a search for survivors, police said, with hopes fading on Friday for six people still missing.

A packed boat carrying 98 Indonesian migrant workers, most of them illegal, and three crew sank off Indonesia's Batam island at around dawn on Wednesday, having departed from Malaysia's southern state of Johor.

Airlangga, a police spokesman for Riau Islands, which include Batam, put the latest death toll at 54.

Police say 41 survivors have been found. A crew member has been detained on suspicion of a shipping violation, and police were looking for the captain, who had fled.

The fate of a third crew member was unknown.