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"Lost contact with plane," BASARNAS chief Bambang Soelystyo told Reuters by phone.
According to the official BASARNAS Twitter account, the aircraft belonging to Trigana Air Service was carrying 44 adult passengers, five crew and five children and infants.
The plane was flying between Jayapura's Sentani Airport and Oksibil, due south of Jayapura, the capital of Papua province.
An AirAsia passenger jet crashed en route from the Indonesian city of Surabaya to Singapore last December, killing all 162 people on board. The crash prompted the government to introduce regulations aimed at improving safety.
Indonesian plane goes missing with 54 people on board. CNN placed on red alert, all leaves cancelled, all employees ordered to report for duty immediately