At least 46 individuals were arrested on Tuesday as police worked across the country to contained planned Azimio protests called by leader Raila Odinga.
Interior CS Kithure Kindiki said in a statement the 46 are suspected to have orchestrated robberies, arson and damage to property.
"All suspects will be arraigned in court tomorrow," Kindiki said.
He said fourteen of the suspects were arrested within Nairobi while 32 were nabbed in different parts of Nyanza region.
The CS further said investigations are underway to arrest other suspects in connection with the chaos witnessed on Tuesday.
Raila had called for resumption of mass protests on Tuesday to continue mounting pressure on government over electoral grievances and cost of living.
The police, however, acted strategically and prevented protesters from accessing the Central Business District, technically dealing the mass action a blow.
The security detail of Azimio leaders, including that of Raila and Kalonzo Musyoka, were also withdrawn.
This was preceded by isolated ugly scenes in parts of the city where a bus was burnt to a shell by goons on Ngong Road and a lorry transporting steel from Mombasa to Kampala torched on Southern bypass.
Further, chaos were witnessed in Eastleigh where the Juja Shell Petrol station was attacked and robbed of 12 gas cylinders.
In parts of Nyanza, protesters engaged the police in running battles as they barricaded roads and damaged vehicle windscreens. The chaotic scenes were witnessed in parts of Kisumu, Homa Bay and Migori.
Kindiki said such incidents foreshadowed "grave danger" to the rule of law and the stability of the country.
"The violence, looting and destruction of public amenities such as roads coupled with disruption of daily activities portend real and imminent danger of our country sliding into irretrievable anarchy," he said.
"These criminal acts must cease."
The CS added that the duty imposed by Section 5(3) and (8) of the Public Order Act Cap. 56, on organisers of protests to assist the police in the maintenance of peace and order was repealed.
This, he noted, had prompted action from the police in line with section 5(2), (6) and (10) of the Public Order Act Cap. 56.
Kindiki said the Ministry of Interior was not going to allow demonstrations that result in injury of persons or damage to property.
"No more violent protests shall be allowed anywhere in Kenya. With or without notices, demonstrations and protests of any type which injure people, security officers, businesses and property shall be prevented at all costs," he said.
Kindiki said security officers had been directed to carry out their mandate fairly and arrest anyone breaking the law regardless of their political affiliation.