A ferry capsized in the strait between the islands of Bali and Java on Friday and TV footage showed passengers standing on its side then jumping into the sea as the boat sank in placid waters.
Official statements about how many people were rescued ranged from 41 to 71.
Didi Hamzar, head of Bali's Search and Rescue Agency, said the ship's manifest listed 51 people on board including 14 crewmen. Passenger boats are frequently overloaded in Indonesia. He told TVOne that 10 people were missing based on the manifest.
Footage broadcast by TVOne showed other ships in the background as the ferry, Tafelia 2, sank in the narrow Bali Strait. It languished on its side before capsizing.
Boats are a popular and relatively cheap form of transportation in the world's largest archipelago nation which spans more than 17,000 islands with a population of 256 million. Sea accidents are common, with safety regulations often poorly enforced.
The ferry was enroute from Gilimanuk port in Bali to Banyuwangi on Java.
A local navy chief Lt. Col. Wahyu Endriawan said a total of 71 people have been rescued without any casualties.
"We cannot yet know whether some were trapped inside the ship which has totally submerged," he told MetroTV.