It warned residents near the Orange River, downstream from the town of Douglas, to be on the look-out for fast-rising water levels.
Douglas is situated at the confluence of the Vaal and Orange rivers.
"It is predicted that at Upington, water levels in the lower Orange River could reach a height of up to 7.9m with a flood peak of 5 300m per second expected on Friday.
"In the Vaal and Orange River catchment, the Vaal Dam is currently 100 percent full and the outflow has been reduced to 780m³ per second. Seven flood gates are now open and will remain open for the next two days."
The Bloemhof Dam was currently at 104%, expected to rise to 110% by January 13. The outflow of the dam is 2 800m³ per second.
"At the Gariep Dam the outflow is 2 000m³ per second and the current capacity of the dam is 115%. The dam is expected to return to a capacity of 100% in just over a week."
The Vanderkloof Dam is at 113% capacity with an outflow of 2 300m³ per second.
Early estimates indicate that around 32 people have died in the recent flooding in Gauteng and KwaZulu-Natal.
Communities were encouraged to listen to their local media continuously for updated emergency information.
"Floods and flash floods can happen quickly without warning so people staying in flood-prone areas must be prepared to act immediately," said the ministry for co-operative governance and traditional affairs in a statement on Wednesday.