"One of our biggest nightmares is the fact that 2010 is going to be held in June when there is a possibility of another bout of H1N1," Motsoaledi said.
The month-long tournament, hosted in Africa for the first time, is expected to attract 450,000 tourists during the South African winter.
Motsoaledi said the department of health had managed to acquire 1.3 million doses of the H1N1 vaccine and another 3.5 million doses from the World Health Organisation (WHO).
"We received a letter from the World Health Organisation that they are going to donate to South Africa 3.5 million doses of H1N1 which will arrive in this country by March," he said, adding that the WHO donation saved South Africa about 250 million rand ($32.48 million).
The WHO, which declared swine flu a pandemic in June last year, has been in discussions with South African government officials on how to reduce the risk of the influenza spreading at the tournament.
The H1N1 virus has spread globally and killed 15,000 people since first appearing in early 2009, according to the World Health Organisation, although the real toll is likely to be much higher.
Pregnant women and people with health problems such as diabetes are the most at risk.
"We are going to be vaccinating...starting with pregnant women, people at entry points, people who are involved in sports administration," said Motsoaledi. He said vaccinations would start soon.
