“If possible stay indoors and off the roads,” it advises. “Never drive on a road covered by water. If the vehicle stalls, leave it immediately and seek higher ground.”
Residents are also advised to move their valuables to a “safe place above the expected flood level”, switch off their electricity at the source, and to move livestock to higher ground.
Wildlife in the national parks are not thought to be at high risk because they tend to instinctively seek out higher land when necessary, rangers say.
In recent days helicopters and the military have been deployed to rescue people in some of the worst-affected areas.
In Limpopo, low-lying bridges have been washed away and some roads destroyed.
Within the Kruger National Park, staff accommodation was submerged by water overnight and workers were evacuated to safety.
The Reuters news agency reports that flooding in south-eastern Africa has become more frequent and severe as climate change makes storms in the adjacent Indian Ocean more powerful.