Tourists were urged to stay clear of the area near the popular Kings Canyon Resort, 320 kilometres west of the Northern Territory town of Alice Springs.
The Central Land Council said the cull would centre on Tempe Downs, a 1,000-square-kilometre former cattle station now owned by the Urrampinyi Iltjitajarri Aboriginal Land Trust.
The council had earlier released images of horses either dead or dying of thirst in the parched centre of the continent.
"Nobody wants to see suffering, especially the traditional owners of the land, who love the horses but are well aware of the terrible consequences of out-of-control populations," council director DavidRoss said in a statement.
Elizabeth Jennings, the president of the Waler Horse Society of Australia, is calling for a stay of execution.
"It's a bloodbath," she said. "There's a huge risk of these horses suffering. They're a moving target and you're shooting them from a moving platform, and to think that you are going to shoot them dead is not how the reality will play out." She said it would be more humane to round up the horses, and find new homes for the fittest animals. The older, sicker horses would be shot at close range.
More than 7,600 people have signed the society's petition.//DPA