Indonesia's Search and Rescue Agency says it is still searching for one of the two "black boxes" from a passenger plane that crashed into a mountain over the weekend, killing all 54 people on board.

Agency chief Henry Bambang Soelistyo said rescuers who reached the crash site on Tuesday had retrieved the cockpit voice recorder, but not the flight data recorder.

Soelistyo earlier said both black boxes had been recovered. But on Wednesday he said officials had misinterpreted reports from rescuers at the scene.

The ATR42-300 twin turboprop plane crashed Sunday into a mountain while on a scheduled 42-minute flight from Jayapura to Oksibil in Papua province.