The boat was carrying more than 50 football players and fans from the western Uganda district of Hoima.
Witnesses say overloading and bad weather are probably to blame for the accident, as rescue attempts continue.
In 2016, about 30 footballers and fans drowned when their boat capsized on Lake Albert.
The passengers were travelling to Runga landing site where a friendly match between two local clubs was scheduled.
The wooden canoe capsized shortly after it departed the docks.
A police spokesperson said that fishermen at nearby landing sites rushed to the rescue and 32 people were rescued within an hour of the accident.
Friends and relatives of the missing passengers have gathered at the shore as police conduct search operations.
The police and Military Marine Unit responded shortly afterwards with divers who have since been able to recover nine bodies, the BBC’s Dear Jeanne reports from Kampala.