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The ministry added that it had established temporary shelters, food and essentials for evacuees, which would be placed at assembly points.
Included in the evacuation were areas near the Nairobi Dam and Titanic Dam. Buildings within the Nairobi River wetland area would be removed, the interior ministry said.
It is unclear how many people will be affected by the evacuation order.
The Kenyan government has faced criticism over the speed of its response to the ongoing natural disaster.
Although President Ruto has said the government would procure land for those who have had to leave their homes, some displaced people are still stranded after their homes were swept away.
The government is yet to release any detail on the evacuation plans, or how people will be notified.
Mr Ruto has defended his administration, telling the BBC on Monday that "a whole-of-government approach is under way".
Following a cabinet meeting on Thursday, Mr Ruto's office said victims of the floods were "increasingly receiving help with food and non-food items" and attributed the extreme weather to climate change.
"[The] cabinet resolved that the government, from now on, will rally the country in implementing measures, programmes and policies that will mitigate the effects of climate change," it pledged.
One of the biggest drivers of the rains is the Indian Ocean Dipole - opposing areas of warm and cold surface water often refered to as the "Indian Niño" because of its similarity to El Niño in the Pacific.
Warmer surface temperatures caused by climate change pushes more moisture and energy into the atmosphere, making weather patterns more erratic and severe.