The torrential rains that have caused widespread flooding and landslides across the country in recent weeks are forecast to worsen in May, Reuters reported.
In a statement, the ministry said further flooding was "expected in low lying areas, riparian areas and urban areas while landslides/mudslides may occur in areas with steep slopes, escarpments and ravines."
The deluges have destroyed homes, roads, bridges and other infrastructure across East Africa's largest economy.
At least 164 people have been injured by the adverse weather, while 212,630 have been displaced, the ministry said.