Images from Rwanda show muddy water sweeping streets and destroying houses in its path.
"Our priority is to reach every home that has been damaged to rescue any trapped people," François Habitegeko, governor of Rwanda's western province, told Reuters.
He adds that the rain picked up on Tuesday night and that the Sebaya River was flooded.
A total of 109 people are estimated to have died in the western and northern provinces.
Floods also in the neighboring country
Six people also died on Wednesday night in neighbouring Uganda near the border with Rwanda, according to the Red Cross.
Uganda has experienced heavy and persistent rainfall since late March and the floods have displaced hundreds of people. In recent days, several landslides have also been reported.