Primary and secondary schools will resume next year in January with a phased reopening of colleges and universities, Education CS George Magoha has announced.
Magoha said stakeholders have also shelved the reopening of candidates in 2021.
The CS confirmed this year's school calendar has been declared null and void due to the coronavirus.
Magoha said all students to remain in there current class in 2021.
"In consultation with Ministry of Health we have agreed schools to reopen when daily Covid-19 cases reduce consistently for 14 days. Social and physical distancing is the most critical factor in ensuring safety of learners," the CS said.
"Inter-county movement of students will cause severe challenges with high incidents of infections. We are happy to inform Kenyans that the president accepted the recommendations."
Magoha was speaking on Tuesday at KICD Nairobi accompanied by Education stakeholders.
He said the universities will only reopen only when they meet the requirements.
"Members of the senate and faculty must agree how they are going to do a phased reopening," he said.
The institutions will undergo an inspection to decide if they have met the required regulations.
Kuppet secretary general Akello Missori said the burden of shouldering the health system should the trend continue will be enormous.
"With children crowding, it will be impossible to think of opening schools," he said.
KNUT secretary general Wilson Sossion said that they have engaged in the process saying that they support Magoha in every decision.
"The flattening of the curve is what will guide us. Safety of learners and teachers at the place of work is very critical and important. We urge all parents to ensure the safety of the children until such a time that schools will be reopened," he said.
National parents association chairman Nicholas Maiyo said Kenya should do away with the 2020 school calendar and reopen in 2021.
"...this is because the academic calendar has been greatly dented," Maiyo said.
President Uhuru Kenyatta had directed Magoha to notify the public on the resumption of the 2020 academic year.
Uhuru in his address to the nation on Monday from Harambee House said the announcement should be made not later than Tuesday.
The proposal to reopen in September was among initial recommendations to President Kenyatta in May by a team formed by CS Magoha.
But this was followed by a second recommendation in June opposing the September reopening and instead calling for reopening in January next year.
The January proposal was supported by stakeholders including teachers' unions and CS Magoha who said schools will not be reopen until the infection curve is flattened.
Magoha explained the recommended January reopening was due to medical advice that "the spike of the infection is expected to occur around the same time (September)."