"It was imperative to get ahead of the curve of this epidemic ten years ago. We all for various reasons have lost ground," Barbara Hogan said at the opening of an international meeting of scientists searching for ways to prevent AIDS.
"It's even more imperative now that we make HIV prevention work. We desperately need an effective HIV vaccine."
Her remarks marked a contrast to those of her predecessor, Manto Tshabalala-Msimang, who was derided as "Dr Beetroot" for championing use of the vegetable to fight the disease.
Hogan took over the ministry in a political shake-up last month, in a move hailed by activists as an end to Tshabalala-Msimang's policies that for years questioned whether HIV causes AIDS.
"We know that HIV causes AIDS. The science of HIV and AIDS is one of the most researched subjects in the medical field," said Hogan, later slamming "wasted time" which contributed to the country's high AIDS prevalence.
Some 5.5 million people in the country of 48 million are living with the disease.
Some 900 researchers and scientists are attending the conference, being held for the first time outside of the United States or Europe.
"This is a country with the greatest number of HIV infections in the world. Nowhere else is the need for a vaccine greater than right here," said conference chair Lynn Morris.
"As we all know the field is at a turning point. One thing is clear, we need to continue with these steps and they need to be bold. The field needs more input, fresh ideas and new directions."
Recent clinical trials, including one launched in South Africa in 2007 and one in America were stopped amid great disappointment after the injections were found ineffective.
Experts believe that a vaccine is the only way to defeat the pandemic, but say that any breakthrough is still years away.