Twenty-eight people were rescued and taken to the Sukabumi immigration office for identification, Brig. Gen. Tatang Zainudin, the National Search and Rescue Agency's operation chief, said by phone from the scene. Among those rescued were three Lebanese nationals who were found early Saturday after being stranded on an island about 20 kilometers (12 miles) from where the boat sank, Zainudin said.
He said 21 bodies were pulled from the water Friday afternoon, including seven children.
A helicopter and more than a dozen boats were being used Saturday to search for about 35 people believed to be missing, but strong currents and high waves were hampering the operation, Zainudin said.
"We fear those who are still missing were unable to survive," he said.
There were conflicting reports about the exact number of people on the boat due to the lack of a manifest, but some survivors told officials that about 100 asylum seekers from Lebanon, Pakistan and Iraq were believed to be aboard, said a local police chief, Lt. Col. Deddy Kusuma Bakti.
Survivors said the boat was headed for Australia's Christmas Island.
Lebanon's official National News Agency said 17 Lebanese drowned in the incident. Nine members of a single family were among the Lebanese victims, with a woman and her eight children dying and her husband surviving, the agency reported.
The boat capsized and sank after being hit by up to 6-meter (19-foot) waves hours after leaving Sukabumi early Friday, Zainudin said.
Australian Minister for Immigration and Border Protection Scott Morrison said in a statement that authorities had received a call Friday morning saying the boat was believed to be about 25 nautical miles off Indonesia's coast. He said Australian authorities then notified their Indonesian counterparts. Australia also put out an all-ships broadcast, and a merchant ship responded but was unable to locate the boat. A Border Protection Command aircraft also was unable to find the vessel.
"Any loss of life is tragic and this latest incident again reflects the dangers of people smuggling," the statement said.
The incident came ahead of new Australian Prime Minister Tony Abbott's first visit to Indonesia next week. He is expected to meet with Indonesian President Susilo Bambang Yudhoyono.
Indonesia has said that the Australian navy's plan to intercept and force back Indonesian fishing boats crowded with asylum seekers could breach Indonesian sovereignty.