The second wave of the virus is expected to hit South Africa before winter.
Health Minister Aaron Motsoaledi's spokesman, Fidel Hadebe, said: "This stock will be used mainly on priority groups such as pregnant women and health workers at the front line of [the fight against] the virus."
He said he could not say exactly when the vaccine would be readily available because of the high demand for it worldwide.
The department is negotiating with at least three international companies for the vaccine.
"There is nothing that stops us from procuring more doses, but this will be guided by the cost."
Hadebe would not say how much the vaccine will cost.
Though the number of swine flu infections has decreased significantly in the past three weeks, the health department has issued a health warning to people travelling to the northern hemisphere.
On Sunday, a 28-year-old pregnant woman from Dubai was admitted to the intensive care unit of a Western Cape hospital with swine flu.
About 91 people have died from swine flu in South Africa, almost 6000 worldwide.
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