The vessel was travelling from the town of Kalemie, in the south-east, to Moba at the time.
"We have collected 10 bodies. The manifest says there were 58 passengers, but they might have been many more," Kalemie's deputy mayor told the BBC.
Bad weather causes many accidents on the lake at this time of year, but rarely is such a big boat affected.
Boating disasters on Lake Tanganyika have become frequent occurrences in recent years.
Correspondents say that due to the poor infrastructure in the war-ravaged DR Congo, ferries are the cheapest and most popular form of transport between lakeside towns.
Alexis Katempa, Kalemie's deputy district commissioner, said an investigation into the accident was under way.
He said that the wooden boat bumped into a rock and sank.
The BBC's Arnaud Zajtman in DR Congo says the boat was called Yote ni Mapenzi ya Mungu, which in Swahili means "everything that happens is out of God's will".