The decision was taken for the safety of children and teachers after some schools were left submerged in water, minister Riziki Pemba Juma said.
The rains have also destroyed property and roads.
More than 350,000 students are currently enrolled in school in the semi-autonomous region of Tanzania.
However, students are still sitting their school-leaving exams, Ms Juma said.
A deluge of rain on East Africa's coast has also reportedly killed 14 people and left 1,500 people homeless in neighbouring Kenya.
All schools on the islands of Zanzibar have been temporarily closed because of flooding following weeks of heavy rains, says the education minister.