There were 54 people, including five crew members, on board the plane, the agency added.
“Because it was night & visibility is limited we suspend search Trigana Air and we continue the search tomorrow morning at 06.00 LT [21:00 GMT Sunday],” the rescue agency wrote on its Twitter account.
A source in one of the Papua province's airlines has also told RIA Novosti earlier in the day that the plane had crashed into a mountain, killing all people on board.
In July, a military transport plane Hercules C-130B crashed crashed into a residential district in the southwestern part of Medan, the capital of the Indonesian province of North Sumatra, about two minutes after it took-off, killing more than 100 people.
In December 2014, AirAsia's Flight QZ8501, flying from Surabaya, Indonesia, to Singapore, lost contact with air traffic control and crashed into the Java Sea, killing all 162 people on board.