Spokesperson Biren Valodia said the test results were received on Thursday from the National Institute for Communicable Diseases (NICD) and confirmed by the Western Cape health department.
Medi-Clinic officially confirmed that "swab and blood tests of the patient that presented himself at Cape Town Medi-Clinic with flu-like symptoms on Monday were negative for the Influenza A (H1N1) or swine flu virus".
The man was placed in isolation as a precautionary measure because he had recently travelled to Argentina and could have come into contact with travellers from areas where the influenza strain was prevalent.
NICD deputy director Lucille Blumberg said in a statement on Thursday that there were no laboratory-confirmed cases of swine influenza in South Africa.
"Five of the samples tested to date have in fact been positive for seasonal influenza.
"Seasonal influenza results in significant illness and mortality and it is very important that persons at risk for complications of influenza should be vaccinated against seasonal influenza before the season."
People at risk included those 65 years or older and those with chest problems and other chronic illnesses. The local influenza season began towards the end of May, with a peak in June or July, she said.
"The vaccine is not thought to protect against swine influenza but will reduce the impact of seasonal influenza," Blumberg said.
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