Update: An Indonesian transport official confirmed the aircraft had been found in the Bintang highlands region, near its intended landing site at Oksibil airport.
It remains unclear if anyone survived. The wreckage was discovered by villagers, who then alerted officials.
"Residents provided information that the aircraft crashed into Tangok mountain," said the Indonesia's director-general of air transportation, Suprasetyo.
An Indonesian registered aircraft belonging to Trigana Air Service aircraft went missing on Sunday over the country's remote Papua province, according to official statements published to Twitter.
The plane had 54 people on board including 44 adults, five children and five crew.
BASARNAS, Indonesia's national search and rescue agency told the media that search efforts for the missing flight had seen "zero outcome" and that it was temporarily suspending rescue efforts for the night due to darkness.
Indonesian Transportation Ministry Spokesman Julius Barata said that the ATR42-300 twin turboprop plane was travelling from Papua's provincial capital, Jayapura, to the city of Oksibil when it lost contact with Oksibil airport's air traffic control.
It left Jayapura at 2:22 pm local time and lost contact with air traffic controllers about 2:55 pm.
Rugged terrain both increases the chances of an accident and makes search and rescue efforts complicated. Some of the mountain peaks in the region are as high as 10,000 feet.