The teams on the ground have so far seen at least 38 bodies at the scene and haven't found any survivors, said Bambang Soelistyo, the head of Indonesia's search and rescue agency.
Helicopters are being deployed to the densely forested area in the eastern Indonesian province of Papua to begin the evacuation process, he said.
The airliner, operated by the Indonesian carrier Trigana Air Service, lost contact with air traffic control Sunday about half an hour into a short flight from the provincial capital to a town in the mountains.
Search planes spotted debris on a mountainside Monday, but efforts to try to reach it on foot and by helicopter were suspended until Tuesday because of fog.
Report of crash from villagers
There was no indication that a distress call was made from Trigana's ATR 42-300 turboprop aircraft before it lost contact Sunday, Indonesian Transportation Ministry spokesman J.A. Barata told CNN Indonesia.
There are many possible reasons for the apparent lack of a distress call, CNN aviation analyst Mary Schiavo said. It could indicate that crew members were too busy dealing with whatever situation arose to send one, or that they didn't realize they were in trouble, she said.
Villagers reported seeing a plane crash into a mountain, according to Indonesian aviation authorities. The site is about 14 kilometers (9 miles) from the airport where the plane was supposed to land, search officials said.
The plane was carrying 44 adult passengers, five children and five crew members when it went missing on the flight between Jayapura, the provincial capital, and Oksibil, an inland town near the border with Papua New Guinea.
All those on board were Indonesian, authorities said.
Few roads, unpredictable weather
The search teams face tough challenges in the dense jungles of Papua's sparsely populated highlands.
Weather patterns are unpredictable in the region, with a tropical climate, tall mountains and moisture coming in from the sea.
Papua has few roads connecting cities, towns and tribal villages. To get where they want to go, people either have to take a plane or a boat -- or walk, which can sometimes take months.
"This is a place where some people still hunt their food with bows and arrows while others buy it in supermarkets," the travel guide Lonely Planet says in its description of the province.
A big part of Trigana Air's business is ferrying people and cargo between different parts of Papua.
Before Sunday's crash, the airline had been involved in 19 serious safety incidents since 1992, according to Flightglobal
, a website that tracks the global aviation industry.
Eight of the incidents resulted in the loss of the aircraft, and the 11 others involved major damage, Flightglobal said.
Airline on EU blacklist
Trigana is one of a large number of airlines banned from operating in European airspace
"because they are found to be unsafe and/or they are not sufficiently overseen by their authorities," according to the European Commission.
It has been on the list since 2007.
The loss Sunday of the Trigana plane is Indonesia's third air disaster in less than eight months.
In December, AirAsia Flight QZ8501
went down in the Java Sea while headed from Surabaya, Indonesia, to Singapore. All 162 people on board were killed.
And in June, an Indonesian military transport plane
crashed soon after taking off from the city of Medan, killing at least 135 people.