The district health inspector, Edward Bugimbi, ordered the closure of Mulabana, Betta and Auntie Vickie nursery and primary schools.
Pupils and teachers who were eager to start the new term were dissappointed when they were told to return home.
The move follows fears of the El Nino rains that prompted health officials to inspect sanitation facilities in the district.
The closure had been effected prior to the opening of the third term with strict instructions to the head teachers to implement the order.
Teachers, some of whom came from distant areas, pondered over the next move as the pit latrines would take long to be constructed. Bugimbi said he could not allow classes to go on in such a dangerous environment.
Teachers at Mulabana complained that construction of the school new premises had delayed.
Construction started three years ago. They blamed Samalia Construction Company that was contracted by the district tender board for the mess.
The old pit latrine collapsed and students had no facility to use.
Most districts have instituted measures in preparation for the highly publicised El-nino rains expected between late September and December. Enda
Schools Closed Over Latrines