They said the delay in opening schools was a major setback for students and called on governments to take precautionary measures such as water and soap to curb the spread of the disease among students.
Both UN agencies say students face the threat of malnutrition and girls being thrown into a frenzy that could lead to pregnancy because the time they spend living at home is nothing.
“School is a protection for children,” said Matshidiso Moeti, executive director of the World Health Organization in Africa.
Only six African countries have opened schools, according to a WHO and Unicef study of 39 countries.
Some countries also open schools only for students writing high school graduation exams.