Water swept away two people, including a child under 10 years old, in the southeast of the city following intense rain on Thursday and Friday, Mamadou Camara from the civilian protection service told AFP.
A third victim, a woman in her 50s, died after a car she was travelling in fell from a bridge and sunk under the water in northern Conakry, Camara added.
The vehicle's driver remains unaccounted for.
Infrastructure Minister Gando Barry visited the scene and asked residents to move away from high-risk areas.
"When you settle in a flood-prone area, you prevent moving water from flowing normally. The only way to prevent floods is to clear the way," he said, announcing measures to implement the recommendations.
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