"Hundreds of houses collapsed, several cereal granaries were damaged and some 2,000 people are homeless," the area's commissariat said in a statement carried on national public radio Monday.
It said more than 165 mm (6.5 inches) of rain fell on Saturday and Sunday, quite an unusual amount for this semi-desert area.
Victims told radio that the rains are the worst to have battered the area in 16 years.
Rescue teams have meantime been dispatched to the area to evacuate the most vulnerable of the victims -- children and the elderly -- trapped by the waters.
Those rendered homeless are being sheltered in schools and other public buildings as officials launched an appeal for emergency aid in the form of food and shelter.
Since the start of the rains in April several people have died and scores wounded in parts of this west African nation.
In June at least five people, three of them members of one family were killed after their houses gave in to heavy downpours in central Pouytenga province.
Two weeks earlier unusual hailstorms wounded five in Oubritenga, a province adjacent to Pouytenga.
In April three school pupils were killed and 30 others wounded after their classrooms were hit by a thunderstorm in the town of Koudougou, about a 100 kilometres (60 miles) west of the capital Ouagadougou.