After previously denying links between HIV and AIDS, the South African government began providing AIDS drugs in clinics last year. As many as five million South Africans are HIV positive, which is more than any other nationality in the world.
The minister in the past has been nicknamed Dr. Garlic because of some of her ideas on combatting AIDS.
After experts said that a new generation of drugs would be cheaper and easier to use, delegates at the 4,000-strong conference came to the defence of ARV drugs.
Fatima Hassan of the AIDS law project at the University of Witwatersrand, was very critical of the govenment and said she thought there was "deliberate campaign against evidence-based medicine." Hassan said that ARVs are saving people's lives.
She says unambiguous messages must come from the highest level, the minister of health, as communities are confused and in particular poor communities.
Mark Nelson, director of HIV services at the Imperial College School of Medicine in the UK said that tackling AIDS without the use of ARVs was "a no-brainer", and it was important to give people the belief that these drugs work because they do.
Earlier in the conference, South African military officials said they were fighting a "human war" against the "formidable enemy" of HIV/AIDS, and said 23% of South Africa's troops are infected with HIV - a similar rate to the adult population at large.
The army is taking part in a US-funded programme to see how AIDS is affecting its combat-readiness, and this includes giving anti-retroviral drugs (ARVs) to some 1,000 soldiers.