Bambang Soelistyo, head of Indonesia’s search and rescue agency said his team had found the aircraft completely destroyed and partially burnt.
The black box flight data recorder has also been found.
Trigana Air plane came down on August 16 in dense forest in a mountainous area, close to its destination of Oksibil.
The plane was carrying 44 adult passengers, five children, and five crew members – all believed to be Indonesian.
It was also said to be carrying about 6.5 billion rupiah ($486,000) in cash, which was due to be distributed to poor families in the area. Officials have not said whether this has been located.
Members of the rescue team – made up of about 100 police, military and civilians – began reaching the site on Tuesday morning.
Bambang Soelistyo told reporters: “The plane was totally destroyed and all the bodies were burned and difficult to identify.”
Bad weather and difficult terrain at the crash site were hampering efforts to remove the bodies but they will eventually be taken to the provincial capital for identification.
Officials confirmed the black box had also been found. It contains data on the plane’s operations and could yield clues as to the cause of the crash.
The ATR42-300 twin turboprop plane took off from Sentani airport in Jayapura at 14:21 local time on August 16, but lost contact with air traffic controllers half an hour later.
Bad weather is believed to have been a possible reason for the crash. A search plane was forced to turn back on the day of the crash because of dangerous flying conditions.
Oksibil, which is about 175 miles south of Jayapura, is a remote, mountainous region, which is extremely difficult to navigate.
Trigana Air has had 14 serious incidents since it began operations in 1991, losing 10 aircraft in the process, according to the Aviation Safety Network.
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