Photos from the scene show the boy conscious and looking into the camera.
The Swiss-made Pilatus aircraft with which he was traveling lost contact with air traffic control on Saturday afternoon, shortly before it landed. Oksibil Airport
The plane operated by private passenger Dimonim Air belonged, had gone from Tanah Merah, about 40 minutes flight south, to Oksibil in the province of Papua, when it went down.
It carried nine people, including two crew members.
According to the AFP news agency, nearby villagers heard a "loud roar followed by an explosion".
An investigation into the cause of the crash is being conducted, officials said.
Airplanes are one of the few ways to get around Papua, a remote and mountainous region that is extremely difficult to navigate.
Due to the rapidly changing weather conditions, however, it is not an easy place to fly.
Three years ago, a Trigana Air-Twin turboprop plane came down near Oksibil, killing all 54 on board.