Transportation ministry spokesman Bambang Ervan said the U.S.-made Kodiak plane belongs to a private religious foundation, Advent, and was carrying seven people when it crashed while taking off from an airstrip.
The five surviving passengers were taken to a nearby hospital, Ervan said. He identified the pilot only as Bob Robert.
The private airstrip is located 20 kilometers (12 miles) southwest of Jayapura, the provincial capital.
Indonesia, a sprawling archipelagic nation of 240 million, has been plagued by transportation accidents in recent years. Overcrowding, aging infrastructure and poor safety standards are often to blame.
Flying is one of the main transportation means in Papua, the second biggest of Indonesia’s more than 17,000 islands.
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