Rescuers were searching for survivors of the Merpati Nusantara Airlines crash just off the coast of Kaimana, said Bambang Ervan, a spokesman for the Indonesian transportation ministry.
There were 21 passengers and six crew members aboard the plane, a turbo-propeller MA60, he said.
Ervan could not immediately confirm any casualties, though a Kaimana Airport ticket agent said that at least 15 bodies have been recovered.
Merpati, a cash-strapped state-owned airline with an aging fleet, flies many of the more remote routes in Indonesia.
In 2010, a Merpati airplane overshot the runway at the Rendai airport in Manokwari, West Papua, injuring 78 people.
A year earlier, two Merpati planes crashed within two months of each other in Papua.
The first occurred in July 2009 when a Merpati flight lost its front wheels as it took of from Biak. A month later, another flight, a Twin Otter aircraft, crashed, killing 16 people on board.
Indonesia has made efforts in recent years to improve its safety record.
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