The plane plunged into the sea with all 189 aboard feared dead. Indonesia is deploying underwater beacons to trace its black box recorders and uncover why an almost-new plane crashed minutes after take-off.
In a statement, Lion Air said human remains were collected in 24 body bags after sweeps of the site of the crash, in waters about 98 to 115 ft deep roughly 15 km off the coast to the northeast of Jakarta.
The bags were taken to a hospital for identification, with more expected overnight, authorities told broadcaster Metro TV.
Drones and sonar technology deployed in Indonesia to search for a Lion Air passenger plane which crashed into the sea on Monday.
Earlier, Indonesian President Joko Widodo met with the relatives of passengers on board.
The president has ordered the search operation at sea to continue round the clock.