Up to 20,000 "bandits" had attacked the biggest city Almaty and had been destroying state property, Tokayev said in a televised address after a week when protests over fuel prices exploded into a countrywide wave of unrest.
He said as part of the "counter-terrorist" operation, he had ordered law enforcement agencies and the army "to shoot to kill without warning."
"The militants have not laid down their arms. They continue to commit crimes or are preparing for them. The fight against them must be pursued to the end. Whoever does not surrender will be destroyed," Tokayev said on state television.
He dismissed calls to hold talks with protesters.
"What stupidity. What kind of talks can we hold with criminal and murderers?" he said.