Speaking in Pretoria, Sefularo said he was confident that the virus would be contained during the World Cup.
South Africa had ordered about 1.3million doses of swine flu vaccine to deal with the expected outbreak, but the WHO offered a further 3million doses to help restrict the spread of the virus.
"Overall, we don't think swine flu will be our biggest challenge. We have learned from last year how to deal with an outbreak so it won't be a major problem," he said.
Sefularo said he hoped the vaccine donated by the WHO would be used starting in April, when South Africa embarks on a national swine flu vaccination drive.
But Sefularo warned that other diseases, such as measles, could be spread in South Africa by World Cup visitors.
He said South African border posts would carry greater risk of disease transfer than airports.
"We believe that a lot of people will be coming into the country through the borders rather than [through] the airports," he said.
"I'm very happy about the readiness around the stadiums but areas of concern are outside Fifa's authorised public viewing spaces, where people will meet in spontaneous gatherings. It's hard to plan for such gatherings," Sefularo said.
Sefularo was updating World Cup health co-ordinators from around the country involved in emergency medical services, hospital services, port health, environmental health, communicable diseases control, health promotion and the military health service.
Pumzile Kedama, the 2010 health readiness head, said the focus was on border posts to ensure that there would not be a disease outbreak.
Exotic foods carried by visitors will be checked.
"We will have port health officers stationed at the border posts to ensure that anyone entering the country is not a health risk," Kedama said.
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