An eight-year-old boy was found dead on the roof of the Small Street Mall on Monday after apparently falling from the Kine Centre, Johannesburg emergency management services said.

The grade three pupil from Finetown in Ennerdale was thought to have fallen after a church service on the 16th floor of the building, spokesperson Percy Morokane said.

He had attended the church service with his aunt, five-year-old sister and another girl, aged four, his father told rescue workers.

"It is alleged that the during the service, the three children requested their aunt to visit the bathroom, and that was the last time they were seen," Morokane said.

The building was searched and they were reported missing to the police.

The two girls were found "unharmed but distressed" on the 18th floor of the building on Monday.

"Further investigations and a detailed search resulted in the body of the boy being found on the roof of the Small Street Mall. Our paramedics declared him dead on the scene."

On Saturday, Sonwabise Mbonyana, seven, survived a fall through the window of a fifth storey apartment onto a concrete roof covered with razor wire in Joubert Park, Johannesburg.

Morokane has urged people to be vigilant when children are in their care, warning that a moment's inattention could cost a life.