The accident in the makeshift mine occurred on Friday in the town of Kamituga, in South Kivu province.
Provincial governor Theo Ngwabidje Kasi deplored "the tragic deaths of 50 people, most of them young".
However, Kamituga mayor Alexandre Bundya said "we are not yet sure of the exact number" of victims.
A local resident who was at the scene, Jean Nondo, told AFP that "according to witnesses, there are more than 50 dead. There is only one survivor."
He said a river close to the mine had flooded after torrential rain.
"Water went into the three tunnels. When people tried to get out, there was no way, as the water was flowing strongly, with high pressure," he said.
Bundya blamed "soil subsidence caused by torrential rain" for the accident.
The mayor decreed a two-day mourning period and called on local residents to help extract the bodies from the ground.
Accidents in DR Congo's makeshift mines are a common occurrence, and are often deadly.
Many such mines are in remote areas, meaning the accidents are under-reported.
The miners sell what they find to local traders, who sell it on to large foreign companies.
"Investigations must be carried out to find out the causes of this disaster," said a representative of the civil society, Nicolas Kyalangalilwa.
"The authorities must take responsibility instead of taxing" these miners.