The Australian-registered Beechcraft civilian plane was flying from Darwin, Australia, to Cebu in the Philippines when it was intercepted by two Sukhoi fighter jets, air force spokesman Hadi Cahyanto told AFP.
It was forced to land at an airport in Manado, on the northern tip of Sulawesi island in central Indonesia, he said.
The pilot and co-pilot, both Australians, were the only people on board.
They were quizzed by military investigators before being handed over to airport authorities for further questioning, Cahyanto said.
“They don`t have a letter of clearance allowing them to enter Indonesian airspace,” he said.
“But because they are civilians not military, we have handed them over to the airport authorities for investigation.”
Transport ministry spokesman J.A. Barata said the aircraft was first sighted over Ambon, the capital of the neighbouring Maluku islands, and had been told to land.
“They paid no attention so they were forced to land in Manado,” he said.
Barata was unable to say what action would be taken against the two men as they were still being questioned.