Three people were confirmed dead while property and infrastructure in the city was destroyed by Saturday's heavy rain.
The four victims, eye witnesses said, included three women, whose car was washed by water currents into a trench in Nyabugogo, a city suburb.
Police, however, put the number of victims at three; identified as Donata Uwimana, a student of Kigali Independent University, and children Adeline Murekatete and another only identified as Chantal.
The mid-afternoon torrential rain came with gusty wind and hailstorm, felling several trees and uprooting roofs of some structures in city suburbs. At least 50 houses were destroyed in Kigali, Police said.
Eye witnesses said the flood almost submerged vehicles, cutting off motorists, who had to park their cars for safety.
"We stopped her, but she ignored us. I think she didn't know how flooded the area was; she kept driving and as she approached, she lost control of the vehicle, which plunged into the trench," an eye witness said of the fate of the victims in the car that was washed into a drainage.
Several vehicles were also damaged, while trees around the city were uprooted and blocked traffic in places such as Camp Kigali near Kigali University Teaching Hospital, main roundabout in the city, and near hotel de Mille Collines.
Also affected was the launch of Fespad arts festival, which was rescheduled to start yesterday.