Professional shooters will begin the cull on Wednesday following an order from Aboriginal leaders in the Anangu Pitjantjatjara Yankunytjatjara (APY) lands.
Locals have complained the animals have been entering communities and wreaking havoc as they look for any available water source, including taps and tanks.
We have been stuck in stinking hot and uncomfortable conditions, feeling unwell, because the camels are coming in and knocking down fences, getting in around the houses and trying to get to water through air-conditioners
Marita Baker, board member of the APY executive, told The Australian.
The animals are also being culled over concerns about greenhouse gas emissions, as the animals emit methane equivalent to one ton of carbon dioxide per year, the paper reported.
A spokesperson for the South Australia Department of Environment and Water said the increasing number of camels had caused several issues in the region.
This has resulted in significant damage to infrastructure, danger to families and communities, increased grazing pressure across the APY Lands and critical animal welfare issues as some camels die of thirst or trample each other to access water
they told news.com.au.
“In some cases dead animals have contaminated important water sources and cultural sites.”
The operation to control the population, estimated to total 1.2 million across the country, is expected to take five days.
Their carcasses will be left to dry off before they are burned or buried, ABC News reported.
Camels were introduced to Australia from India and Afghanistan during the 19th century and used for transport and construction.
If the culling did not take place their population would double every eight to 10 years.
It comes amid estimates that more than a billion animals have died in the wildfires which have been raging across the country.
Chris Dickman, an ecologist at the University of Sydney, told HuffPost earlier estimates nearly half a million creatures had perished were conservative, as they did not include animals such as bats, frogs and invertebrates.
Including those animals, he said it was “without any doubt at all” the losses exceeded 1 billion, which he called “a very conservative figure”.
Conservationists and wildlife experts fear the bushfires may have wiped out entire species of animals.
Populations of small marsupials called dunnarts and glossy black cockatoos may have disappeared entirely after fires burned a third of Kangaroo Island, which has since been described as a “scorched wasteland”.