Earlier, Tertius Zongo, the prime minister, said that 150,000 people across the country had been left homeless.
"We have been able to find shelter for about 110,000 people but there are others who have taken refuge with their neighbours," he said.
Many residents of the capital piled whatever belongings they could salvage in the street after their homes were destroyed by the flood waters and the accompanying mud.
Aid groups said the flood water had smashed bridges, dams and washed away roads, making their task even more difficult.
"Bridges and dams have been destroyed, the main hospital in Ouagadougou which is close to a dam was inundated and some patients including about 60 children were evacuated," Rosine Jourdain, of the Belgian Red Cross in Burkina Faso, said.
"An electrical plant was also destroyed so I think we are going to have some power supply problems."
Some reports said that among the patients moved out of the capital's main hospital were those with infectious diseases.
The government mobilised the army to help firefighters and police deal with the crisis.
Seasonal rains from June regularly cause fatal floods and mudslides in West Africa.
In 2007, over 800,000 people were affected, some 300 died while homes, crops and infrastructure were washed away.