"Based on information UNHCR has received so far from the authorities and refugees, 41 people were rescued and 98 bodies recovered" after Saturday's disaster, the refugee agency said in a statement.
"As many as 250 people may have been aboard the boat," added the UNHCR, which reported that the vessel had been transporting Congolese refugees returning to their homeland from Uganda.
The Ugandan media on Saturday reported 19 deaths in the accident.
The survivors were taken to the Bundibugyo district, to the southwest of the lake, where they have been taken under the wing of the Ugandan state and the UNHCR and its partner agencies, according to the statement.
Relatives have come from the DRC in a bid to identify family members at the nearest hospital.