Fifty-one people on board the plane, operated by DRC's Hewa Bora Airways, survived the crash, which occurred at the airport of Kisangani, a city in the country's northeast, according to the ministry.
The ministry added that the airline had underestimated the total number of people on board earlier in the day and had also reported an incorrect number of casualties and survivors.
According to Hewa Bora Airways, the plane, a Boeing 727, went down into dense forest in Kisangani when the pilot tried to land the aircraft in stormy weather but failed to touch the runway.
Rescue efforts were already underway at the scene, but the dense forest posed much difficulty, local media reported.
The accident is the latest in a series of air disasters in the Central African country. In April, a UN commuter aircraft crashed while trying to land in Kinshasa, killing 32 people. Another air accident killed 20 in the southwestern town of Bandundu last year.
In 2008, a DC-9 airliner operated by Hewa Bora crashed into a residential and market area when taking off from the eastern city of Goma, leaving 44 dead.
Once a popular choice for short- and medium-haul routes, the Boeing 727 first flew in 1963. More than 1,800 had been manufactured when production of the model ended in 1984