It was the second such incident in the area in a little over a week.
The motorised canoe, which left Panyimur on the Ugandan side of the 20km wide lake with 31 passengers aboard, sank on Sunday as it approached Mahagi on the Congolese side, an official in Mahagi said.
He blamed strong winds for the accident, the official, Christophe Ikando, said.
“These boatmen do not want to be controlled. That’s why they come at night to unload,” he added.
“But unfortunately they ran into a fierce wind and all the occupants died except one, the pilot.”
A search was under way to try to recover more bodies, he added.
Late last month, 10 people died and one went missing after another boat sank on Lake Albert.
Such accidents are frequent in this huge central African country, which is dotted with lakes and rivers.
They are caused by overcrowding, pilot inexperience, the absence of lights on vessels, faulty beacons on waterways.
The country’s transport minister Marie-Laure Kawanda was fired after a series of such accidents in April and May.