"A total of six people died in separate incidents including a member of the... police services," Oscar Mabuyane, the Eastern Cape provincial premier said in a statement, updating the death toll.
The policeman died conducting rescue and recovery operations.
Sudden rains pounded parts of the southern province including East London, on the Indian Ocean coast, on Saturday.
Within hours, low lying areas were severely flooded, a local government official told AFP.
Among the worst hit was Mdantsane, a sprawling township on the outskirts of East London.
Scores of people mainly in Mdantsane have been displaced and some roads are "completely submerged making access to distressed communities that much more difficult," the statement said.
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