The environment minister proposed a package of measures Wednesday to slow rampant elephant population growth - including limited killing and contraception - but stressed there would be no mass slaughter.
The elephant population of 20,000 is growing at a rate of more than 6 percent per year, disrupting the delicate biodiversity in the flagship Kruger National Park and other wildlife parks, Environment Minister Marthinus van Schalkwyk said.
He said the government proposed introducing new management measures, including removal of elephants to other areas, creation of special enclosures to protect other species, expansion of parks, contraception and culling.
"I would have preferred not to consider the options of both culling and contraception," he said, but added that the reality left him with no choice.
He said slaughter would only be considered as a last resort.
"The government will never give a blank check to culling," van Schalkwyk told journalists at the Addo Elephant Park.
Environmental groups and other interested parties have until May 4 to comment on the proposals and even after that it may take many more months to bring the measures into force.The initial reactions was positive.
The World Wildlife Fund said it recognized the problem posed by elephant overpopulation in southern Africa and hailed the government's consultations with conservation groups.
"Although WWF does not advocate culling as the preferred management alternative, we recognize that it is a management option and reiterate our view that all other options should first be explored," said Rob Little, acting chief executive of WWF South Africa.
The International Fund for Animal Welfare welcomed van Schalkwyk's promise to invest more into scientific research.
"We dearly hope this indicates a long-term intention to ensure an ethical approach to elephant management," the fund said.
Wednesday's announcement followed months of impassioned debate, with some conservationists arguing that overall biodiversity should take priority and animal welfare groups outraged at the prospect of slaughter.
South Africa has been hugely successful in managing its elephant populations, once on the verge of extinction. But herds in the Kruger Park, and also smaller parks such as Addo, are expected to double by 2020.
"We can conserve elephants but we have to start to worry about what we conserve with it," said Graham Kerley, an elephant expert who works with officials at Addo National Park, which has some 450 elephants.
The country destroyed 14,562 elephants between 1967 and 1994. Without that cull, the population would have rocketed by now to 80,000, according to park estimates. On current trends the population is expected to reach 34,000 by 2020 if it is not curbed.
Van Schalkwyk declined to predict how many elephants might be shot if culling gets the green light. But he said there were more sophisticated management options than before 1994, such as improving fencing and expanding parks.
"There is a huge difference between what we had then and now," he said.
The contraception option is fraught with problems. A female normally breeds every four years and doesn't mate while nursing. With contraception, a female comes on heat every four months - but doesn't become pregnant - and so suffers the physical stress of frequent copulation with bulls four times her weight.
Relocating elephants is expensive. Conservation experts say there are signs that elephants are beginning to move from the Kruger into Mozambique, where populations are more sparse because of movement of people in the long civil war, thanks to the removal of national fences in a new trans-frontier park. But space is limited.
There is no regional consensus on the issue. South Africa, Namibia and Botswana all have booming elephant populations, while East African nations such as Kenya are struggling. Trade in ivory has been banned since 1989 to try to combat poaching despite appeals by South Africa to resume sales and invest the proceeds in its parks.
Botswana has by far the biggest elephant population, with an estimated 165,000 elephants, according to van Schalkwyk. He said Zimbabwe was host to about 80,000.