Learners will have to bear a burden following the three-day demonstrations by the Opposition.
Students will lose up to 20 hours of lessons after orders to close schools over planned protests.
In a statement, Education CS Ezekiel Machogu directed that schools in Nairobi, Mombasa and Kisumu should be closed until further communication is issued.
Interior CS Kithure Kindiki and Machogu said they had received credible intelligence indicating that school-going children in the three cities were at risk.
Demonstrations that took place last week saw more than 50 students teargassed at Kihumbuini Primary School due to protests.
Knut secretary general Collins Oyuu called for dialogue between President William Ruto and ODM leader Raila Odinga decrying the disruption of the school calendar.
"These demonstrations have adversely affected the smooth running of the education calendar in the affected cities and towns mores o schools situated in slums," Oyuu said.
He added that more than 1 million Grade 7 students have been affected by the riots as they can't proceed with their new curriculum.
"It's just the beginning of 2023, our Std 8 pupils are also being prepared for KCPE exams, while the Form 4 students are also getting ready for KCSE," he said.
"We, therefore, call upon the involved parties to embrace dialogue to enable our school calendar to proceed uninterrupted.”
