"I can confirm that all the passengers were killed when the plane exploded as it crashed into the sea," a navy officer involved in the search told ElShinta radio.
"The aircraft was smashed to pieces... We found 15 bodies floating on the water and the other passengers are trapped inside the wreckage." A transport ministry spokesman earlier said there were 27 people on board the Merpati Nusantara airlines MA-60 aircraft, 21 passengers and six crew.
The twin turbo-prop plane took off from Sorong city in West Papua province for Kaimana district about 400 kilometres to the south, he said.
The vast Indonesian archipelago relies heavily on air transport and has one of Asia''s worst air safety records.