Professor Jim Bishop says the second wave of the H1N1 virus is expected to come through in the next few months and is likely to be earlier than the usual flu outbreak.
"At the end of our first wave of swine flu, we saw that the great majority of the population didn't get swine flu and they're still unprotected," Professor Bishop told reporters in Canberra on Saturday.
"So we don't want to repeat everything we saw last year. We have the opportunity to totally dampen the program of having to treat people with swine flu."
Vaccinations are now available for children over the age of six months and are administered through two doses.
Three million doses were taken up within the first two months of the swine flu vaccination being made available.
"We've now put out around seven million doses, so we're building up the immunity of the population which is a good thing. But now we're all back to school, we're facing another winter, this is a good time to get a vaccination."
In the United States, 95 per cent of the flu in the second wave was swine flu, he said.
"Now we don't know how it will pan out in Australia, but we expect that the dominant strain will be swine flu - the same as in the United States."
There was still uncertainty around the second wave being more dangerous, he said.
"But we don't want to reproduce all of the effort that the EDs (emergency departments) ... had to put in last year. We want to eliminate that as this year's scenario."
About 100 cases were identified in November, and that number dropped in December, he said.
Prof Bishop said the greatest hospitalisation rate in last year's outbreak was in children under five years of age - 64 per 100,000 people.
"These children were being hospitalised more than we'd normally see with seasonal flu," he said.
"Yes, we do recommend children get vaccinated."
Prof Bishop said there was good evidence to suggest the vaccine would still work even during the second wave and would keep on working.
"There's no evidence that there's anything new happening that will not allow us to have a successful vaccine."
Canberra GP and Australian Medical Association (AMA) federal councillor Paul Jones said about 80 per cent of the population currently were not vaccinated against swine flu.
There were 191 deaths of people with swine flu in Australia last year and the median age was 53 years, compared to 83 for seasonal influenza.
About 200 cases of swine flu worldwide, according to the World Health Organisation, were resistant to antiviral drugs.
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