The Trigana Air flight lost contact with ground control at 14:55 local time (05:55 GMT) as it flew from the capital Jayapura to the town of Oksibil.
Indonesia's transport minister said the aircraft had been found in the Bintang highlands region, not far from its intended landing site at Oksibil airport.
It is not yet known if anyone survived.
The wreckage was discovered by villagers, who then alerted officials.
"Residents provided information that the aircraft crashed into Tangok mountain," said the country's director-general of air transportation, Suprasetyo.
The ATR42-300 twin turboprop plane was carrying 44 adult passengers, five children and infants, and five crew.