The Trigana Air ATR 42 turboprop plane lost contact just before 3pm (6pm NZT) after taking off from Sentani Airport in Papua's capital, Jayapura, on a 258km flight to Oksibil, a remote settlement in the mountains that is accessible only by air.
It was carrying 44 adults, five children and five crew on the flight, which should have taken 45 minutes.
Just 10 minutes before it was due to land, the plane contacted Oksibil control tower asking to descend, according to Captain Beni Sumaryanto, Trigana Air's director of operations. But it never arrived.
Half an hour later, Trigana Air sent another turboprop plane over the same route to look for the aircraft. "But the weather was very bad, it could not find it and the plane was turned back to Sentani," he added.
"Oksibil is a mountainous area where weather is very unpredictable. It can suddenly turn foggy, dark and windy without warning.
"We strongly suspect it's a weather issue. It is not overcapacity, as the plane could take 50 passengers."
According to Wikipedia, Trigana Air commenced operations in 1991. It has a fleet of 15 aircraft and flies to 21 destinations throughout Indonesia.
Indonesia has had its share of airline woes in recent years. The sprawling nation of 250 million people and 17,000 islands is one of Asia's most rapidly expanding airline markets, but is struggling to provide enough qualified pilots, mechanics, air traffic controllers and updated airport technology to ensure safety. From 2007 to 2009, the European Union barred its airlines from Europe because of safety concerns.