The tragedy happened last evening at the Abu Naima school in the Bukuru area to the south of the city, said Mohammed Abdulsalam, from the National Emergency Management Agency (NEMA).
"Five people died: four students and one female teacher. Twenty-four people - 21 girls and three boys - were injured and taken to hospital," he told AFP.
Two of the children who died were boys and two girls. Their ages were not immediately available, said Abdulsalam.
Heavy rains earlier in the day saw many children stay away from the school, which caters for pupils aged five to 10, he added.
"The rescue operation was concluded last night at about 10 o'clock (2100 GMT). We are going this morning for further checks," he explained.
Building collapses are common in Nigeria, particularly during seasonal rains. Sub-standard building materials and lack of planning permission are often contributory factors.
Last year, 116 people, most of them South Africans, were killed when a guesthouse for foreign followers of popular pastor and televangelist TB Joshua collapsed in the financial capital, Lagos.
Extra floors were being added to the building at the time.
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