The accident occurred in the Kagade region on Wednesday night. According to police, only one person has been found alive.
Searches continued throughout the day, while the cause of the accident was investigated by marine police.
"Possible reasons are that the boat was overloaded, that the journey took place at night, and that the vessel was not seaworthy," police write.
The exact number of people missing cannot be determined, as there is no passenger list.
Boat accidents are common on river voyages in Uganda and on Lake Victoria.
