Interior CS Kithure Kindiki has vowed to deal with alleged criminals infiltrating peaceful demonstrations to loot.
The CS said security agencies will remain alert to intercept and thwart harm to the public.
Kindiki added that attacking critical infrastructure and the emblems of the country's sovereignty will not be tolerated.
This comes after the Tuesday protests were marred with violence with many reporting lootings in their businesses.
"The organisers of today’s orgy of violence in parts of Nairobi, Mombasa and several other parts of the country are reportedly planning to repeat their anarchic chaos and cruel plunder on Thursday and Sunday this week, and perhaps much more frequently in the future," Kindiki said.
"This reign of terror against the people of Kenya and the impunity of dangerous criminal gangs must end at whatever cost. The Government is determined to stop criminals aiming to terrorise the public and harm Kenya, notwithstanding attempts to politicise crime."
The CS assured the public that the planners, executors and financiers of large-scale arson, violent robberies and other felonious crimes would be brought to justice.
Kindiki commended the police for acting professionally and with restraint in the management of extremely provocative situations that arose in the course of the violent riots.
"The government commends all law enforcement officers who continue to discharge their challenging mandate of preventing crime and protecting the lives and property of the people of Kenya," he said.
He said that claims of instances of unlawful conduct by law enforcement officers will be investigated and appropriate action taken.
The CS added that the June 25, 2024, protests left a trail of destruction and unprecedented civil unrest in Nairobi and several other towns in the country.
As a result, he said, lives were lost, property worth billions of shillings destroyed or looted, and an attempt was made to burn down Parliament Buildings.
He said the unrest initiated democratic expression of public disapproval of the Finance Bill 2024 which led to the termination of the Bill.
Kindiki said alleged criminal gangs continue to pose a grave danger to the public, riding on announced plans for peaceful protests to disturb public order, commit arson, obstruct public transport and terrorise Kenyans.