The Gardasil vaccine will be rolled out to boys aged 12 and 13 in schools nationally from next year.
It's expected 870,000 boys will receive the HPV vaccine in the first four years at a cost of $20 million, said the Federal Minister for Health Tanya Plibersek.
Plibersek said the vaccine had already had a significant impact on rates of cervical cancer in Australia women.
Vaccinating boys is expected to further reduce those rates by restricting the spread of HPV through sexual transmission.
The health minister said more than 65 million doses of the vaccine had been administered safely to women around the world.
"We know that it's a safe vaccine."
The introduction of the rubella vaccination in 1993 reduced the reported cases of that virus from 5000 in one year to just 10 over eight years, she said.
Two years after the immunisation program was introduced to girls, research showed a 59 per cent drop in genital warts in young Australian women.
Other research showed the rate of high-grade cervical lesions in women had reduced as a result of vaccination, Plibersek said.
"It's expected extending the vaccination to boys will further contribute to protecting the whole community against HPV and indeed will protect a whole generation," she said.
Cancer Council Australia chief executive Professor Ian Olver said it was an important initiative that would benefit the whole community.
The vaccine had no untoward side-effects and was proven to reduce HPV-related lesions, he said.
"It's a long-term strategy and the minister and the government are to be commended for adding to the work that they've already done," he told reporters in Brisbane last week.
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