"Each year, 100,000 children contract the AIDS virus in South Africa, and half of them die before the age of two," UNICEF's representative in the country Macharia Kamau told journalists.
HIV/AIDS is the leading cause of child mortality in South Africa, and accounts for between 40 and 60 percent of all deaths nationwide, UNICEF said.
Some 5.4 million people were infected with HIV/AIDS as of 2006, amounting to almost one fifth of the total population.
The grim statistics mean South Africa is not on track to meet the UN's Millennium Development Goal of cutting under-five mortality by two thirds by 2015. Instead, child mortality rose by an annual 5.8 percent in the ten years between 1990 and 2000, the organisation said.
"We are not confident to reach the targets of the MDG's, concerning infant mortality, maternal mortality and HIV/AIDS," Kamau said.
"I don't think that the message has been down to the communities," he added.
South Africa's government and in particular its President Thabo Mbeki have been fiercely criticised in the past for their policies on AIDS, in particular a reluctance to promote the use of anti-retroviral drugs.
Health minister Manto Tshabalala-Msimang, often called Dr Beetroot for calling for the use of vegetables to combat AIDS, stirred controversy at the International AIDS Conference in Toronto last August after South Africa displayed garlic and beetroot at its stall.
At the time, UN Special Envoy Stephen Lewis called Pretoria's AIDS polices "more worthy of a lunatic fringe than of a concerned and compassionate state."