
Assailants opened fire as the Smart Air-operated craft touched down at an airport in South Papua on Wednesday, killing the pilot and co-pilot, according to the transport ministry.
A ministry statement said all 13 passengers, including an infant, were unharmed.
A preliminary investigation suggested the attack was linked to an “armed criminal group”, said a joint military-police task force, using a designated term for armed rebels in Papua.
Faizal Ramadhani, head of the Cartenaz Peace Task Force handling Papua separatist rebels, said in a statement that “the authorities are still hunting down the group of perpetrators suspected of being involved in the action.”
Flights at the domestic Koroway Batu airport have been suspended until further notice, he added.
Papua, which shares its main island with Papua New Guinea, is a former Dutch colony that declared independence in 1961.
Indonesia, however, took control two years later, followed by a 1969 referendum in which 1,000 Papuans voted to integrate into the country.
Papuan independence activists regularly criticise the vote and call for fresh polls, which Jakarta has rejected, citing UN support for its sovereignty over Papua.