Unveiling statistics that minister Aaron Motsoaledi admitted "destroyed my soul," he added that four percent of schoolboys have the virus.
"It is clear that it is not young boys who are sleeping with these girls. It is old men," the Sowetan newspaper quoted Motsoaledi as saying.
"We can no longer live like that," he said.
Motsoaledi called for an end to the trend of young girls becoming involved with "sugar daddies."
Motsoaledi also revealed that 94,000 South African schoolgirls fell pregnant in 2011, some aged as young as 10.
South Africa has one of the world's highest HIV/AIDS infection rates, although the number of cases resulting in death is in sharp decline.
Official figures show that South Africa has six million people living with HIV, in a population of 50 million.
The country has the largest anti-retroviral programme in the world, serving 1.7 million.
The health department recently introduced measures to curb the spread of HIV among school children, introducing voluntary testing and suggesting condom distribution at schools.
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