A search plane spotted the wreckage Monday, but a ground team hasn't yet been able to reach it, said Raymond Konstantin, an official for Indonesia's search and rescue agency.
Authorities had said earlier that villagers in a remote area of Indonesia's eastern Papua province reported seeing the passenger plane crash into a mountain.
It's the Southeast Asian nation's third air disaster in less than eight months.
The ATR42-300 turboprop aircraft operated by Trigana Air Service was carrying 44 adult passengers, five children and five crew members when it went missing during a short domestic flight Sunday. All of those on board were Indonesian, authorities told CNN Indonesia.
Ground team heading to area
The search over rugged, densely forested terrain was halted overnight because poor weather and a lack of light made an already dangerous landscape even more challenging.
A second search plane has been dispatched to verify the debris spotted Monday, Col. I Made Susila Adyana, an Indonesian Air Force official in Papua, told the national news agency Antara.
He said a ground team is heading to the area from the town of Oksibil, the intended destination of the Trigana flight.
The flight lost contact with air traffic control in Papua on Sunday afternoon, the search and rescue agency said on Twitter. It had left Sentani Airport in Jayapura at 2:22 p.m. and was scheduled to land in 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.
Barata said there was no indication that a distress call was made from the plane. He said he would be flying from Jakarta to Papua along with investigators and search and rescue officials.
Thunderstorms in the mountains
There are many possible reasons for the apparent lack of a distress call, CNN aviation analyst Mary Schiavo said. It could indicate that flight crew members were too busy dealing with whatever situation arose to have time to send one, or that they simply didn't realize they were in trouble.
Officials said the weather was clear when the plane took off in Jayapura, but CNN meteorologist Ivan Cabrera said there were some thunderstorms over a mountainous area in the flight path.
The weather could get worse in the coming days, possibly impeding rescue efforts in an area with mountain peaks as high as 3 kilometers (10,000 feet).
"The terrain is going to be an issue as well, as we have some pretty steep slopes here," Cabrera said.
Trigana banned from flying in Europe
The Trigana Air Service plane is the third Indonesian aircraft to crash in the past 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.
Trigana Air Service 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.