According to reports, the twin-propeller plane came down in the city centre shortly before it was due to land in heavy rain at Goma airport.
The government said it was not immediately clear how many people were on board the Fokker 50, which was loaded with cargo.
Early reports suggested as many as 30 people had died.
Government spokesman Lambert Mende said later said the number of dead stood at nine people.
"For the moment we have counted nine dead, passengers and crew. No one on the ground was killed. The plane fell in an empty space, and because of the rain, no one was around. It was really lucky," Mende said.
CAA, who operated the plane, told the Reuters news agency that there had been five confirmed deaths - all crew members.
Another person was missing.
DR Congo has a poor air safety record and the runway in Goma has not been fully repaired following a 2002 volcanic eruption left it covered in ash.
The flight was arriving from the town of Lodja, some 440 miles (700km) to the west in Kasai-Oriental province.
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