Mountain villagers had reported hearing a loud noise they thought could be a crash soon after the disappearance of flight 518, Gerardo Rojas, a civil defence official said on Friday.
Venezuela's civil aviation authority said the aircraft was carrying 43 passengers and three crew members.
The passenger list included a well-known Venezuelan political analyst and relatives of a senior government official, authorities said.
Jorge Alvarez, president of Santa Barbara, said the 20-year-old aircraft was well maintained and had no record of technical problems.
The pilot had worked with the airline for eight years and received special training for flying in the Andes, Alvarez told Globovision, the television station.
"I have to believe the pilot was certainly both competent and well-suited" for the flight, he said.
The aircraft was an ATR 42-300, a turboprop aircraft built by French-Italian company ATR.
The ATR 42 series has been involved in at least 17 accidents since first flying in 1984, according to the Aviation Safety Network, a private air safety monitoring agency.
Thursday's incident was the second reported involving a Venezuelan flight this year after an aircraft carrying 14 people, including eight Italians and one Swiss passenger, crashed into the sea close to a group of Venezuelan islands in January.