The plane's black box recording device was also found, according to the Indonesian Ministry of Transportation.
Recovery efforts were slowed by fierce weather and rugged terrain.
The Trigana Air Service turboprop plane was carrying 49 passengers and five crew members from Jayapura to the city of Oksibil when it lost contact Sunday.
Five children, including two infants, were among the passengers.
Indonesia has had a string of airline tragedies in recent years. In December, all 162 people aboard an AirAsia jet were killed when the plane plummeted into the Java Sea as it flew through stormy weather on its way from Surabaya, Indonesia's second-largest city, to Singapore.
The Associated Press contributed to this report.