"There have been 23 people killed," Alassane Bocoum, the national director of social development, told AFP, adding that all had been identified.
He said thousands of people had been made homeless after around 100 houses were destroyed in several hours of heavy rain yesterday in the city of around two million people.
The worst damage was done to poorly-constructed homes on drainage sites on the banks of the Niger river.
"A monitoring group has been set up to get people to abandon homes built largely of dried mud that could collapse," Bocoum added.
Entire streets and several bridges across Bamako were submerged as motorcyclists and pedestrians found themselves caught up in flash flooding.
Bamako mayor Konte Fatoumata Doumbia said two schools equipped with mattresses and mosquito nets had been set up as emergency shelters for the homeless, the state-owned national daily newspaper Le Progres reported.
But other residents were wandering the streets, not knowing where to go for help, it said.
"We lost everything: cereal, materials, clothes. This is a disaster," Sory Ibrahima Dabo told the paper.
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