Much higher rainfall than usual caused by the La Niña weather phenomenon, which also struck Brazil and Australia, has killed 123 people in South Africa, as well as devastating thousands of homes and farms.
Municipalities in eight of the country's nine provinces have been declared disaster zones.
"All indications seem to indicate that we need to prepare ourselves for similar patterns of what we are seeing, at least for the next couple of months", said Elroy Africa, Director General of South Africa's Department of Cooperative Justice.
Maphaka Tau at the Social Development Ministry told a parliamentary committee that flooding since mid-December could have been better dealt with.
"We have a situation which is not normal in our country and if we were well prepared I think we would have dealt with it much better," he said.
The country's biggest dam, the central Gariep, is already 112 per cent full, whilst the Vaal Dam reached 100 per cent capacity on Wednesday.