The boat, bound for the regional capital Goma, capsized overnight on Tuesday, after having set off in the dark overloaded and from an illegal mooring, regional government spokesman Claude Basila said.
Deadly boat accidents are common in Congo, which has few tarred roads across its vast, forested territory and where vessels are frequently loaded well beyond their capacity.
The spokesman said the boat had 51 passengers on board, of whom 46 were rescued, three died, leaving two missing.
However, survivors who were rescued by local boatsmen said the vessel had been carrying at least 100 passengers.
“A big wave knocked it over and there was nothing more but screams,” said Daniel Mutukura, who trod water for five hours before being rescued.
“I realised a lot of people had drowned because there were more than 100 people on board,” he told Reuters.
A survivor, Mubatiza Mukanirwa, said his wife and children had drowned. He estimated the boat had been carrying nearly 250 people, while another survivor thought 200 had been on board.
“It hurts so terribly,” Mukanirwa said.