By nightfall, there was no trace of the Twin Otter plane, which lost contact with officials on the ground as it flew over Papua at a height of 9,500 feet (2,895 meters), said Transportation Ministry spokesman Bambang Ervan.
Police said they would start a land and air search operation at first light Monday.
The plane Sunday was on a 50-minute journey from Sentani, a major airport in Papua, to the town of Oksibil, said Capt. Nikmatullah, the director of operations of the airline operating the plane, Merpati Nusantara.
The aircraft was carrying enough fuel to keep it in the air for 3½ hours, said Nikmatullah, who goes by a single name. When dark fell, it had been missing for around eight hours.
Indonesia, a nation of more than 18,000 islands, has seen a string of air crashes in recent years.
In 2007, the European Union banned all Indonesian carriers from landing in the bloc. It recently lifted the ban on four of them, including Garuda, the country’s flag carrier, saying standards had improved.
Travel by aircraft is the only way to travel around Papua, much of which is covered with impenetrable jungles and mountains. In the past, crashed planes there have never been found.