Heavy rains across the region have also destroyed homes, crops and some infrastructure.
Flooding as a result of recent heavy rains has killed almost 200 people across Kenya, the government says.
The water has also washed away 8,000 acres of crops and some vital infrastructure.
Neighbouring Uganda, where Lake Victoria has reached unprecedented levels, has also felt the impact of heavy rains, which are expected to continue for weeks.
East African countries have also been hit by a locust invasion and Covid-19.
The authorities in Kenya have told people in some of the affected areas to move away from "potential danger".
In western Uganda, rivers have burst their banks, causing people to flee for safety to the town of Kasese, the Daily Monitor newspaper reports.
In recent weeks, the rising levels of Lake Victoria have forced shoreline communities to abandon their homes and caused erosion along the River Nile, which is fed by the lake.
Last month, a huge floating island of loose vegetation triggered a nationwide blackout in Uganda after clogging a turbine in a hydroelectric power station.
At the end of last year, rain-triggered disasters, including flash floods and landslides, killed at least 250 people and affected some three million people across East Africa. BBC