"At 1:40 local time the Trigana Air black box was found," Transportation Ministry official Julius Arivada Barata told the Reuters news agency by text message on Tuesday.
Operations director at Indonesia's National Search and Rescue Agency, Major-General Heronimus Guru, told a news conference in the capital, Jakarta, on the same day that all passengers on the plane were dead and their remains were being put into body bags and recovered.
Officials have declined to comment on the cause of Sunday's crash until the results of an investigation by the national transport safety committee, but Guru said the terrain in Indonesia's easternmost province may have been a factor.
"There's a possibility the aircraft hit a peak and then fell into a ravine because the place that it was found is steep," Guru said.
Plane was carrying money
There were 44 adult passengers, five children and infants and five crew on the short-haul flight from provincial capital Jayapura south to Oksibil town.
The aircraft was also carrying about $470,000 destined for remote villages, as part of an assistance programme. There was no suggestion the money was somehow linked to the crash.
All on board were Indonesian, officials said.
The aircraft made its first flight 27 years ago, the Aviation Safety Network says. Trigana Air Service has a fleet of 14 aircraft, aged 26.6 years on average, according to the airfleets.net database.
Trigana has had 14 serious incidents since it began operations in 1991, online database Aviation Safety Network says. Besides the latest crash, it has written off 10 aircraft.
Indonesia has a patchy aviation record, with other two major crashes in the past year.
Source: Agencies