Earlier, the National Search and Rescue Agency (BASARNAS) said a twin-turboprop plane had lost contact with air traffic control as it flew over the forested area of eastern Indonesia but efforts to trace it were difficult because of failing light.
Trigana Air Operations Director Beni Sumaryanto said that within 30 minutes of hearing that the aircraft was missing, the airline sent another plane to scour the same flight path but it had found nothing because of bad weather, local media reported.
According to the official BASARNAS Twitter account, the aircraft, a short-haul ATR 42-300 airliner belonging to Trigana Air Service and built in France and Italy, 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.
Air transport is commonly used in Papua, Indonesia's easternmost province, where land travel is often impossible.
According to the Aviation Safety Network, an online database, the ATR 42-300 that went missing made its first flight 27 years ago. ATR is a joint venture between Airbus and Alenia Aermacchi, a subsidiary of Italian aerospace firm Finmeccanica.
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The airline has been on the EU's list of banned carriers since 2007. Airlines on the list are barred from operating in European airspace due to either concerns about safety standards or the regulatory environment in their country of registration.
The airline has a fleet of 14 aircraft, according to the airfleets.com database. These include 10 ATR aircraft and four Boeing 737 Classics. These have an average age of 26.6 years, according to the database.
Trigana has had 14 serious incidents since it began operations in 1991, according to the Aviation Safety Network. Excluding this latest incident, it has written off 10 aircraft.
Airline officials were not immediately available to respond to enquiries from Reuters.
Indonesia has a patchy aviation safety record and has seen two major plane crashes in the past year, including an AirAsia flight that went down in the Java Sea, killing all on board.
The AirAsia crash prompted the Indonesian government to introduce regulations aimed at improving safety.
Indonesia's president promised a review of the ageing air force fleet in July after a military transport plane crashed in the north of the country, killing more than 100 people.