The trial has been branded a public health risk by an environmental group that claims the vaccine due to be tested is a potentially dangerous kind of genetically modified organism (GMO).
But HIV/Aids researchers say the "candidate" vaccine has been thoroughly tested in laboratories and, if successful in humans, could represent one of the most important medical breakthroughs ever.
The trial, the first to test a vaccine fully developed in South Africa, is due to start at sites in South Africa and the US later this year and is part of the South African Aids Vaccine Initiative.
The vaccine is a combination of five HIV genes inserted into a host smallpox virus to be injected into 36 healthy HIV-negative volunteers. They will be monitored for 12 to 24 months in the hope that the vaccine does no harm.
It is the second HIV/Aids South African vaccine trial to generate huge international interest as scientists rush to find an equivalent to vaccines that helped conquer polio and smallpox.
The Department of Agriculture on Friday confirmed receiving a formal objection to the trial from the African Centre for Biosafety, an outspoken critic of GMOs. The objection hinges on safety concerns about GMOs - particularly a new kind of GMO vaccine - which some scientists say are not fully understood. The new multigene GMO vaccine could combine with other viruses to create new viruses, and set off a "worst-case scenario" - the breakout of a virus capable of harming people, objectors say.
Comment: In light of the fact that the smallpox vaccine likely triggered the AIDS epidemic, these fears aren't unfounded.
"There is evidence in the literature that this kind of virus may infect human cells," said Mariam Mayet, environmental activist and anti-GM lobbyist. "This means it is not a completely dead vaccine. If something goes wrong we have to live with the consequences."
South African molecular biologist William Stafford urged caution this week: "The uncertainties are huge because you can generate totally novel viruses whose properties you don't know - it's a total black box."
But HIV/Aids researchers said the objections were ill-founded and should not derail what could be one of South Africa's greatest research triumphs.
Glenda Gray, a world-renowned HIV/Aids researcher and head of the national vaccine initiative, said: "We've done everything that any other vaccine developer would do because we don't want to take any shortcuts."
She said other genetically modified vaccines were saving lives worldwide.