The Indonesia Air Transport plane lost contact with air traffic control at about 1.30pm local time on Saturday around Maros region in South Sulawesi province, Andi Sultan, an official at the local rescue agency, told Reuters.
The aircraft had been heading to Makassar, the capital of South Sulawesi, after departing from Yogyakarta province before contact was lost, Sultan said.
There were eight crew and three passengers on board, he added.
Around 400 personnel, including military and police units, were deployed to search for the plane and those on board, though the effort was being hampered by bad weather, Sultan said. He declined to comment on the possible cause of the incident.
"We suspect the plane came down near the peak of Mount Bulusaraung. We have deployed our personnel there," he said.
The plane had been chartered by Indonesia's Ministry of Marine Affairs and Fisheries, ministry official Pung Nugroho Saksono told state news agency Antara.
Marine Affairs and Fisheries Minister Sakti Wahyu Trenggono said the three passengers were ministry staff conducting air surveillance on fisheries.
The ATR 42-500 is a regional turboprop aircraft capable of carrying between 42 and 50 passengers.
According to unconfirmed Flightradar24 data, an aircraft matching the description was flying eastward over the Java Sea at about 3,350 metres before rapidly losing altitude and dropping off tracking systems.
In France, Franco-Italian planemaker ATR said it had been informed of an accident in Indonesia and that its specialists were supporting local authorities as they began their investigation.
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