Valter Mioto, the mayor of a small Amazon town, said on Saturday that the airliner, carrying 155 people, had crashed in the forest in Peixoto de Azevedo municipality.
"From the information we have, the plane fell on Jarina farm," Mioto said.
"Hospitals in the region are ready to receive the injured."
Infraero, Brazil's airports authority, said the smaller aircraft, an executive jet, landed in the town Serra do Cachimbo even though it had suffered wing damage after the mid-air collision on Friday.
Gol flight 1907 left Manaus in north-west Brazil at 1836 GMT but did not arrive in Brasilia at 2112 GMT as scheduled.
Celso Gick, a spokesman in the Amazon region for Infraero, said the Boeing 737-800 was carrying 149 passengers and six crew members.
Brazilian radio station CBN said at least 20 passengers were employees of Japan's Yamaha Corp.
Five air force jets have been sent to search for the missing aeroplane. Jose Carlos Pereira, Infraero's president, said: "The air force is in the area of the collision."