Much of Papua is covered with impenetrable jungles and mountains. Some planes that have crashed there in the past have never been found.
Dudi Sudibyo, an aviation analyst, said that Papua is a particularly dangerous place to fly because of its mountainous terrain and rapidly changing weather patterns. "I can say that a pilot who is capable of flying there will be able to fly an aircraft in any part of the world," he said.
European plane maker ATR said in a statement late Sunday that it "acknowledges the reported loss of contact" with the Trigana flight "and is standing by to support the relevant aviation authorities."
ATR, based in Toulouse, France, makes regional planes with 90 seats or less.
Indonesia has had its share of airline woes in recent years. The sprawling archipelago nation of 250 million people and some 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 Indonesian airlines from flying to Europe because of safety concerns.
Last December, all 162 people aboard an AirAsia jet were killed when the plane plummeted into the Java Sea as it ran into stormy weather on its way from Surabaya, Indonesia's second-largest city, to Singapore.
That disaster was one of five suffered by Asian carriers in a 12-month span, including Malaysia Airlines Flight 370, which went missing in March 2014 with 239 people aboard during a flight from Kuala Lumpur to Beijing.
Trigana Air Service, which commenced operations in 1991, had 22 aircraft as of December 2013 and flies to 21 destinations in Indonesia.
Associated Press writers Ali Kotarumalos and Angela Charlton in Paris contributed to this report.
This story has been corrected to show that Susanto is the head of Papua's search and rescue agency, not the national search and rescue agency.