The vessel had been loaded with traders and their goods heading from Mugote in South Kivu province towards Goma, the capital of neighboring North Kivu.
A Mugote police official said heavy winds had caused the boat to capsize some 20 kilometers (12 miles) into the journey.
Another local official, from South Kivu, said the boat was carrying around 150 passengers, 80 of whom managed to escape.
He said the bodies of three women and three children had been recovered, while the search operation was still ongoing.
DR Congo has few passable roads, and transport on lakes and rivers is essential for getting around the vast region.
However, shipwrecks are common in the area.
