Defence Minister Waldir Pires told Bandeirantes television the collision appeared to be due to human error. "Only distraction by the crew seems to explain the collision," he said, adding that both planes had modern equipment, and that the area of the collision was well covered by radar.
But other officials said the cause of the crash remained unknown.
Jose Carlos Pereira, president of the Infraero company, which runs Brazilian airports, said the Boeing 737-800 collided with a small executive jet over the Serra do Caximbo area, a densely forested, remote area of northern Brazil's Para state.
"Landing there would be a high-risk operation, but amazing things can happen in aviation, so we keep hoping," Globo television's online service quoted Mr Pereira as saying.
Infraero said the pilot of the smaller plane had managed to make an emergency landing and transmit information about the collision.
Civil aviation authorities said Flight 1907 of the GOL discount carrier was reported missing several hours after leaving the Amazonian city of Manaus in the afternoon, on a flight headed to Brasilia and then on to Rio de Janeiro.
Airborne search parties, using planes and helicopters were dispatched to the area where the plane was feared to have crashed, authorities said.
Two Brazilian Air Force planes with 20 people aboard, and two helicopters headed to the crash area, using infrared equipment to detect signs of the plane, but would have to wait until daylight to conduct a visual search.
Local hospitals were put on full alert, in case casualties are found.
Dozens of relatives of passengers aboard the jetliner rushed to Brasilia's airport hoping to get information about the fate of their loved ones.
There were conflicting reports about the exact number of people aboard the plane, but authorities said the number was around 150.
GOL, an airline created in 2001, only confirmed that the plane was missing.
The airline, Brazil's leading discount carrier services some 50 domestic destinations as well as neighboring Paraguay, Uruguay, Argentina, Bolivia and Chile.