There was chaos when a group attacked and chased a team of government officials demolishing houses in riparian areas in Mukuru slums, Nairobi.
This is after it emerged the eviction team may have killed at least two children in the area in the process of their actions, police said.
This angered locals who grouped and chased the team from the scene, officials said.
Among the dead was a five-year-old boy who was crushed by rubbles after a structure fell on him in the area.
Another body was discovered in the rubbles hours later on Sunday, police said adding they are investigating the incident.
Separately, a 17-year-old boy was killed by another eviction team in Mathare slums on Monday.
This sparked protests in the area hours after President William Ruto had left the area.
The president had visited the area to cope with those affected by the floods.
The team evicting the families from the affected areas later embarked on the mission before the body of the teenager was discovered sparking the protests.
Police used teargas canisters to disperse the protesters before they picked up the body of the boy at the mortuary.
According to police, the Mukuru incident happened after the group of about 50 approached the multi-agency team demolishing houses and evicting those living near the riparian land in the area on Sunday and ordered them to leave.
The team was accompanied by police officers who tried to stop the chaos in vain.
The officers shot into the air and used tear gas canisters in vain.
Police said the protesters pelted the team with stones and twigs forcing them to retreat.
One excavator was damaged in the chaos. It was later carried on a lorry from the scene.
This forced the team to stop their operation.
In the incident that happened on Sunday, locals said the victim was picking up their valuables when he was fatally injured in the head.
Tension is mounting in the areas targeted with resistance growing.
Police say the affected have to move for their safety in general.
The victims say they want to be given an alternative place to stay as they are being evicted.
Ruto said those evicted would be given Sh10,000 each, food and bedding.
The developments were prompted by ongoing rains and flooding which have killed more than 230 people.
In Nairobi, more than 40 people have been killed and dozens displaced.
The reopening of schools has been postponed over the rains.
At least 230 people have so far lost their lives due to the ongoing heavy rains and resultant floods across the country.
Interior Cabinet Secretary Kithure Kindiki said about 164 people were injured and 72 were missing after the floods.
“A total of 41,526 households have been displaced affecting approximately 212,630 people. 138 camps have been set up across 138 Counties hosting 62,061 people.”
Approximately 227,238 people have been impacted by the heavy rains.
Additionally, Kindiki says a total of 1,967 schools have been affected by the floods.
The government says multi-agency teams drawn from the Kenya Defence Forces, National Youth Service, and humanitarian agencies had already hit the ground running to coordinate rescue efforts and provide essential help to the displaced people.