The move could hurt the country's tourist industry, with animal welfare lobbies calling for a tourist boycott to protest the decision.
South Africa slaughtered more than 14,500 elephants from 1967 to 1995, before halting the practice because of global pressure.
"We will allow culling in certain parts of the country. But there is no intention of wholesale slaughter," Environment Minister Marthinus van Schalkwyk said.
The guidelines call for "humane" killing, specifying that a rifle of at least .375 caliber be used. Sharpshooters usually kill entire herds because of the complex social structure of elephants and because young animals need to be taught social behavior by adults in order to survive.
Although elephants are endangered in other parts of Africa, the population in South Africa is robust. But the issue of culling is emotional for many people, because of elephants' keen intelligence and elaborate social behaviors. Elephants are known to grieve for their dead.
There are 18,000 elephants in South Africa, including about 12,500 in Kruger National Park, one of the country's top tourist attractions. SANParks, the government agency in charge of parks and national game reserves, called for culling in a 2005 report to the government, arguing that too many elephants threaten other species.
Van Schalkwyk said there was also concern about the impact of elephants on the landscape and the livelihoods and safety of people living near the herds.
Before culling, reserve managers will have to prove that they have excess elephants and that killing is the only effective option.
Animal Rights Africa said culling was "cruel and morally reprehensible."
"The latest research has proved that elephants have a sense of self-awareness, placing them in a unique category with great apes, dolphins, and humans," the organization said. "How much like us do elephants have to be before killing them becomes murder?"
Christina Pretorius, a spokeswoman for Cape Town-based International Fund for Animal Welfare, said her group did not believe that other options to culling had been properly examined in Kruger National Park, such as the creation of "transfrontier parks" to allow elephant populations to roam freely from one country to another.
Proponents of transfrontier parks say that as elephant populations wander, season by season, the environment can recover.
Products In Action
South Africa is home to about 18,000 elephants, such as these in Tembe Elephant Park. The nation calls for the killing of entire herds to reduce their population. (associated press/file 2007) 
