In a televised address from State House, Ruto said the demonstrations had been "hijacked" and he was putting "on notice the planners, financiers, orchestrators, abetters of violence and anarchy".
He added that the military had been deployed across the country “in response to the security emergency caused by the ongoing violent protests".
“This marks a critical turning point in how we respond to such threats on national security," he said.
“Today’s attack resulted in the loss of lives, destruction of property and a lack of respect for the institutions, the head of state said.
It is still not clear how many people have died but the Kenya Medical Association counted five people.
Many of those injured are receiving treatment at the Kenyatta National Hospital.