The accident occurred on Thursday on waterways leading to the district of Darak, an island in the Lake Chad Basin near the border with Chad, where seasonal floods have made boats the only viable means of getting around.
Mamat Zarma, divisional officer of Darak, said the wooden boat was en route when it was rocked by violent winds, causing it to capsize.
"So far, we have recovered the bodies of five women and 13 men," Zarma told Reuters by telephone, adding that the exact number of passengers onboard at the time of the accident was unknown.
He said search and rescue operations were ongoing to find other possible missing people.
Two weeks ago, a similar incident occurred in the nearby district of Goulfey, when a locally-built canoe carrying around 30 passengers capsized, killing four people and leaving others missing.
Heavier-than-usual seasonal rains in parts of West and Central Africa have caused widespread floods, including in Cameroon's Logone and Chari division, which includes Darak and Goulfey.
This has forced locals to rely on water transport to get around, but a lack of canoes encourages overcrowding - the most common cause of boat accidents in the area.
While the rainy season is drawing to a close across a large part of West and Central Africa, many countries are still grappling with the fallout from the flooding, which killed more than 1,520 people, affected around 7.2 million others, and had swamped 960,000 hectares of cropland as of Nov. 20, according to the U.N. humanitarian agency OCHA.
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