"According to the (local) community, the Trigana Air plane hit Mount Tangok in Pengunungan Bintang district," Xinhua quoted Suprasetyo, director general of the air transport of the transport ministry, as saying in a press conference held at the ministry in Jakarta.
The Trigana Air Service ATR-42 flight left Sentani Airport in Papua region's capital Jayapura at 2:22 p.m. and was scheduled to land in the southern town of Oksibil at about 3:16 p.m., officials said.
The plane lost contact at about 2:55 p.m., Transportation Ministry spokesman J.A. Barata told CNN Indonesia.
The aircraft was carrying 44 adults, five children and a five-member crew.
"A search was launched earlier today, but was called off because of bad weather, and it's also now dark there," Barata added.
Military officers, policemen and other search and rescue personnel in Papua province participated in the coordinated search efforts, Transport Minister Ignasius Jonan said.
"Tomorrow (Monday), (they) will take action as earlier as possible," he told the press conference.
"Tonight (Sunday night), those officials from the search and rescue office along with director general of the air transport will go there to help handle evacuation," Jonan said.
It was unclear why the plane crashed into the mountain. Officials said the weather was clear when the plane took off in Jayapura.
Trigana Air has had 14 serious incidents since it began operations in 1991, losing 10 aircraft in the process, the Aviation Safety Network said.
It has been on a European Union (EU) blacklist of banned carriers since 2007, the network added.