The accident occurred Friday evening on Lake Mugesera in Rwamagana District. The boat was carrying passengers, mainly farmers who were returning from harvesting their produce in the Rukumberi sector in Ngoma district, heading to Rwamagana district, when it blew a strong wind.
The boat capsized before it sank, according to local officials.
"As of Saturday evening, 14 bodies were recovered, and two others who were still unaccounted for were recovered on Sunday," Rwamagana District Mayor Radjab Mbonyumuvunyi told Xinhua.
Forty-seven people were on the boat when it sank, not 46 as reported earlier, he said.
Marine officers rescued 31 people.
Mbonyumuvunyi said the boat was overloaded with passengers and agricultural produce including maize and beans, as several people were returning from harvesting their produce across the river.