The four-day symposium in the east coast city of Durban had a rowdy opening ceremony with members of the audience taunting South African Health Minister Manto Tshabalala-Msimang with comments like "shame on you" and "AIDS treatment now" as she addressed the delegates.
The government has come under heavy criticism for failing to roll out a national treatment plan for AIDS sufferers, choosing instead to focus on "nutritious diets" as a way to fight the disease for those infected.
Tshabalala-Msimang proposed that Aids sufferers eat garlic, onions, olive oil and African potatoes to boost their immune systems.
She said in a BBC interview that nutrition and the use of traditional medicine was the focus of the government's efforts to treat the epidemic.
Nutrition remedy flawed
A recent report from the University of Stellenbosch said that most patients given an extract from the African potato actually became more ill after initial signs of improvement, while raw garlic could increase internal bleeding and interfere with drugs, and olive oil had no proven effect.
Children hold a vigil for AIDS victims
There has been outrage over South Africa's Medicines Control Council which is threatening to ban the antiretroviral drug nevirapine, expressing doubts over its safety - despite the fact that UN agencies and the World Health Organisation endorse the medicine.
Organisers of the conference, sponsored by South African campaigners and business leaders, are hoping the government and activists will settle their differences for the remaining three days and find common ground on how to prevent the spread of the disease.
Conference chairman Jerry Coovadia said lessons learnt at the conference would be important for the rest of Africa, the continent most affected by AIDS.
"It is time to stop, take stock and talk to each other. From this meeting we hope to develop a cohesive idea of where we are in fighting the epidemic," Coovadia said.
Of the world's 42 million people infected with HIV or full-blown AIDS, 29.4 million live in sub-Saharan Africa, which had 3.5 million new infections last year, and 2.4 million AIDS-related deaths.
South Africa has one of the highest AIDS rates in the world with UNAIDS estimating 360,000 deaths in 2001 - an average of 986 per day.
Activists to sue government
South Africa has an estimated 4.7 million people infected with HIV/AIDS out of a total population of around 44 million.
HIV/AIDS is expected to cut South African life expectancy from an estimated 59.9 years in 1990 to 45.2 years in 2005.
13 percent of South African children were estimated to be orphans in 2002, many of them because of HIV/AIDS.
An estimated three percent of South African households are currently headed by children.
Tshabalala-Msimang, who faces a looming legal battle with an AIDS lobby group, Treatment Action Campaign (TAC), for failing to implement a national treatment plan for all AIDS sufferers, has defended the state's policies, dismissing the criticism as unfair.
"We must engage each other to find solutions to this problem but not to play political games on such a sensitive and emotional subject."
An AIDS specialist at South Africa's Human Sciences Research Council (HSRC), Olive Shisana, said that by 2010, South Africa's gross domestic product would be 17 percent lower because of AIDS.
According to the 2002 Nelson Mandela HSRC study of HIV/AIDS, an estimated three percent of South African households were headed by children.
"The problem being the worst in urban informal settlements, where HIV was found to be most prevalent," Shisana said.