• Government spokesman Cyrus Oguna on Wednesday pleaded with the residents to move to schools on higher grounds.
Rain-triggered disasters, including flash floods and landslides, have killed at least 132 people and affected nearly half a million others across the country since October.
Thousands of people in 32 counties are resisting pleas to abandon their homes, and properties, which are slowly being marooned by floodwaters.
Some of the villages could also be destroyed by landslides.
Government spokesman Cyrus Oguna on Tuesday pleaded with the residents to move to schools on higher grounds, where government help is awaiting them.
"We are issuing an advisory that those living in the high-risk areas such as Lake Victoria Basin, Lower Tana Delta, Coastal and Central regions to move to safer areas," he said.
The United Nations has set aside Sh300 million to assist people affected by floods, mudslides and landslides as a result of the heavy rains.
A statement by the UN's Office for the Coordination of Humanitarian Affairs on Monday said the funds will be channeled to humanitarian response initiatives targeting worse hit areas where lives have been lost and people displaced.
West Pokot, Makueni, Kitui, Teso South, Mandera, Turkana and Elgeyo Marakwet are among the worst affected places.
In Nairobi, several parts of the county have flooded following heavy rains throughout the weekend.
Governor Mike Sonko said 30-year-old sewer lines in informal settlements will be expanded starting January.
The rapid expansion of informal settlements without sewerage coverage has led to the disposal of human waste in the open.
In Ol Kalou, four families have expressed concerns of disease outbreak after their homes were flooded because the authorities ordered overflow water directed to their residence.
They alleged the Ol Kalou municipal board has directed that all the water spilling from commercial and residential buildings in the town be directed to the toilets within the building.
Board chairman Mwangi Nyaga could not be reached for comment as his phone was engaged.
The tenants said they are forced to wear gumboots to access their houses or go out.
Those who do not have gumboots are forced to remove their shoes and walk barefoot through the dirty water.
They expressed fear that if the rains persist, human waste could find its way into their living rooms.
They called on the Ol Kalou municipal board chairman to visit the plot.
In Taita Taveta, 300 families have been displaced following floods over the weekend.
A Voi-based activist on Tuesday said he will sue the National construction authority (NCA), Nema and county government for approving construction of residential houses on riparian land along Voi River.
Waki Jarongo, an environmentalist, said the agencies should be held accountable for the loss of property amounting to millions of shillings, following the Sunday floods that rendered close to 300 families homeless in Tanzania, Mnaoni and Msambweni Estates in Voi subcounty.
The families living near Voi River were displaced after their houses were submerged by raging water after the river burst its banks.
They are now camping at Voi Primary and Kalela Primary schools.