The ATR 42-500 turboprop owned by aviation group Indonesia Air Transport lost contact with air traffic control on Saturday about 1.30pm local time (0530 GMT) around the Maros region in South Sulawesi.
There were seven crew members and three passengers on board the plane, which was chartered by Indonesia's Marine Affairs and Fisheries Ministry to conduct air surveillance on fisheries.
The passengers were ministry staff members.
Authorities had initially said eight crew members were on board but later revised the figure.
The plane was flying to Makassar, the capital of South Sulawesi, from Yogyakarta before losing contact.
On Sunday morning, local rescuers found the wreckage in different locations around Mount Bulusaraung in the Maros region, South Sulawesi rescue agency official Andi Sultan said.
The mountain is roughly 1500km northeast of the sprawling island nation's capital, Jakarta.
"Our helicopter crews have seen the debris of the plane's window at 7.46am," Sultan said.
"And around 7.49am, we discovered large parts of the aircraft, suspected to be the fuselage of the plane," he said, adding the tail of the plane was also seen at the bottom of the mountain slope.
Rescuers have been deployed to the locations where the wreckage was discovered, Sultan said, adding the search was hampered by thick fog and mountainous terrain.
On Sunday afternoon, rescuers found a crash victim's body in a ravine around 200m from Mount Bulusaraung's peak, Sultan said.
The status of the other nine people on board was not yet known.
The head of South Sulawesi's rescue agency, Muhammad Arif Anwar, had said that after finding the wreckage, the priority was to find the victims, with 1200 personnel to be deployed to search for the missing.
Indonesia's National Transportation Safety Committee (KNKT) head Soerjanto Tjahjono said the agency's initial findings indicated the aircraft had crashed into the mountain's slope.
"We call this controlled flight into terrain. The pilot was able to control the plane and the crash was not intentional," Soerjanto told local media in Makassar.
Investigators have yet to determine the cause of the crash, he said.
KNKT did not respond to Reuters' request for comment.
Aviation experts say most accidents are caused by a combination of factors.
The ATR 42-500, manufactured by Franco-Italian plane maker ATR, is a regional turboprop aircraft capable of carrying between 42 and 50 passengers.
Flight tracking website Flightradar24 said on X the surveillance plane was flying over the ocean at a low altitude, so its tracking coverage was limited, and the last signal was received at 0420 GMT, about 20km northeast of Makassar airport.
It was the first deadly ATR 42 crash in Indonesia in more than a decade.
In 2015, a Trigana Air Service ATR 42-300 crashed into a mountainside in Indonesia's Papua region, killing all 54 people on board.
