Reuters reports that two further outbreaks were detected in the central province of Gauteng, home to the city of Johannesburg, and Mpumalanga, a province in the north.
"The affected areas have been placed under quarantine and the provincial veterinary services are applying the necessary disease control measures," the ministry said in a statement, adding it was investigating the source of the disease and what other farms could be affected.
The first outbreak outside South Africa's control zone for ASF was detected in April and were thought to be linked to contact with wild animals. The disease was found on a farm in North West province, killing 32 out of a herd of 36 pigs on a farm in the Ditsobotla district, with the remaining animals slaughtered, reports said.
The ministry said the same virus was responsible for all three outbreaks.
African swine fever is incurable in pigs but harmless to humans. It has spread across China since last year, causing major losses to the world's largest hog herd.