The ministry said all students would resume studies in their current classes.
Education Minister George Magoha said no final-year national examinations would be held for primary and secondary pupils this year.
Those exams are usually held in October and November each year.
However, colleges and universities will prepare to re-open in September this year with strict guidelines, the minister says.
Schools across Kenya closed in March after the country's recorded its first coronavirus cases.
On Monday, Kenya's President Uhuru Kenyatta reopened the borders of three counties that had been closed as part of the lockdown.
He then gave the education ministry 24 hours to give guidelines about the school calendar.
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