Heavy rains have hit large parts of the country, and the deluge is expected to continue, according to the national weather service.
The government has "declared a national state of disaster to enable an intensive, coordinated response to the impact of floods" affecting the seven provinces, mainly on the east coast of the country, the statement said.
Disaster management centres report seven deaths so far but no national toll has been announced.
Five people died in the south-eastern KwaZulu-Natal province, said Nonala Ndlovu, spokeswoman for the provincial disaster management department COGTA.
A newborn baby is among those who died, COGTA said in a statement.
Several other people are missing after they tried to cross a swollen river.
Two more people were reported dead in northeastern Mpumalanga province, local authorities reported.
In northern Limpopo, a hospital, roads, and bridges were damaged, while cars were washed away.
"In agriculture, farmers have suffered crop and livestock losses," read the statement from the presidency.
Last year, South Africa was hit by its worst floods in living memory, which left more than 400 people dead in the third-largest city Durban and surrounding areas.
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