Floods have hit the city's ninth district, on its southern fringes, after the swollen Chari river burst through dikes, the International Organization for Migration (IOM) said.
"It is now urgent that we scale up efforts to quickly provide suitable shelter and emergency response support to the disaster victims," said Anne Schaefer, IOM's local mission chief.
"There is concern for COVID spread in tight living spaces as well as risk of water-borne diseases that are endemic in the region."
The Chari, which flows through the Central African Republic, Cameroon and Chad, is one of Lake Chad's main sources of water.
It has typically has high flows between August and November after the rainy summer months.
The IOM, a UN-related agency, has helped to provide temporary shelter for the displaced.
But it says much more needs to be done to support those most in need, including with food, sanitation and education.
"It's the first time in years that we have had such heavy rains," said IOM spokesman Francois-Xavier Ada Affana.
More than 393,000 people have been displaced in the Lac province due to flooding and attacks by jihadists, IOM added.
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