Indonesia's transport ministry says it has received reports that the wreckage of a missing plane carrying 54 people has been found by locals in a remote region of Papua.

The Trigana Air flight left Papua's capital Jayapura yesterday afternoon, bound for Oksibil, the capital of a remote mountainous region near Papua New Guinea.

The plane lost contact with air traffic controllers about 10 minutes short of its destination.

Last night transport minister Ignasius Jonan and ministry officials told reporters that locals had reported seeing the plane hit a mountain.

Search and rescue teams were preparing to scour mountainous, heavily forested terrain in rugged eastern Indonesia.

Heavy cloud initially delayed plans for an aerial survey to locate the plane.

"The weather is good, no problem. All flights are ready to go," said Pratu Susilo, the operator at Sentani airport from where an aerial survey was due take off.

A search team on land, meanwhile, set out from Oksibil on Sunday (local time).

A spokesman for the ministry told ABC News the plane was carrying 49 passengers, including two children and three toddlers, and five crew members.

There was no immediate word on whether anyone survived.

The search for the plane was officially suspended at nightfall last night, but recovery crews including aerial surveillance teams will resume operations again this morning.

"The latest information is that the Trigana aircraft that lost contact has been found at Camp 3, Ok Bape district in the Bintang Mountains regency," Air Transportation director-general Suprasetyo, who goes by one name, said in statements quoted by the Reuters news agency.

"Residents provided information that the aircraft crashed into Tangok mountain."

The Trigana Air plane disappeared earlier on Sunday during a short flight from Jayapura at 2:22pm local time (3:22pm AEST) for what should have been about a 40-minute flight to Oskibil.

Oskibil is a remote settlement in the mountains, about 40 kilometres from the Papua New Guinea border, and only accessible by plane.

Ten minutes before it was due to land at 3:00pm (local time), the plane contacted Oksibil control tower asking to descend, Trigana Air's service director of operations captain Beni Sumaryanto said.

But the plane never arrived.

Half an hour later, Trigana Air sent another turboprop plane over the same route to look for the missing aircraft, he said.

"But the weather was very bad, it could not find it and the plane was turned back to Sentani," Captain Sumaryanto said.

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."

Map Map of flight path of missing Indonesian plane

Trigana on EU blacklist of carriers since 2007

Trigana Air is a small airline established in 1991 that operates domestic services to around 40 destinations in Indonesia.

According to the Aviation Safety Network, an online database, the ATR 42-300 had its first flight 27 years ago.

ATR is a joint venture between Airbus and Alenia Aermacchi, a subsidiary of Italian aerospace firm Finmeccanica.

Trigana has been on the European Union blacklist of banned carriers since 2007.

Airlines on the list are barred from operating in European airspace due to either concerns about their safety standards, or concerns about the regulatory environment in their country of registration.

Trigana Air has a fleet of 14 aircraft with an average age of 26.6 years, according to the airfleets.com database.

These include 10 ATR aircraft and four Boeing 737 classics.

Trigana has had 14 serious incidents and written off 10 aircraft since it began operations in 1991, according to the Aviation Safety Network's online database.

Small aircraft are commonly used for transport in remote, mountainous Papua, and bad weather has caused several accidents in recent years.

On Wednesday, a Cessna propeller plane operated by Indonesian company Komala Air crashed in Papua's Yahukimo district, killing one person and seriously injuring the five others on board.

Officials suspect that crash was caused by bad weather.

Indonesia has a patchy aviation safety record and has seen two major plane crashes in the past year, including an AirAsia flight that crashed into the Java Sea during stormy weather in December, killing all 162 people on board.

That crash prompted the 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.

ABC/wires