The affected schools are Salondo, Malabo and Nakaywe which are located in the flood plains.
Mongu District Education Board Secretary Mulonda Sendoi confirmed the development to ZANIS in Mongu on Friday.
Sendoi explained that some of the affected pupils have been integrated into nearby schools that are not affected by the floods.
He said other schools such as Lealui and Makuku are also affected by the floods but are still open for learning.
Sendoi, however, expressed worry at the water and sanitation conditions.
He encouraged guardians of the affected pupils to make an effort and enrol the children in schools that are not affected by the floods which are perennial.