A South Australian ecologist has raised alarm over changes to the way wild dogs are managed, saying a new policy could lead to dingoes becoming "functionally extinct" in some areas.

Key points: The SA Government wants to introduce aerial baiting and rebuild parts of the dog fence

The SA Government wants to introduce aerial baiting and rebuild parts of the dog fence An ecologist says the new policy could harm native dingoes

An ecologist says the new policy could harm native dingoes A sheep farmer has expressed strong support for the proposal

The SA Government's proposed changes are in response to concerns wild dog populations have increased both north and south of the state's dog fence in the past two decades, putting the livestock industry at risk.

Wild dog management is enforced by the dog fence, a 5,400-kilometre structure that in many places is over 100 years old.

South of the fence, wild dogs are considered a pest and strictly controlled, while north of the fence they are considered to be native dingoes and only controlled when they reach problem numbers.

The South Australian Government's proposed measures include rebuilding large parts of the fence, imposing minimum baiting standards on all landholders south of the fence and allowing aerial baiting across the state.

Dr Katherine Moseby says proposed changes could harm dingo populations. ( Supplied: Katherine Moseby )

But University of New South Wales ecologist Katherine Moseby questioned whether there was a genetic difference between dingoes and wild dogs.

"They're calling it a wild dog policy but really it's dingoes," Dr Moseby said.

"Dingoes in South Australia are one of the purest forms of dingoes in Australia so really we're talking about dingoes, we're not talking about feral dogs."

The Government is also offering a new bounty of $120 for every wild dog killed by landholders.

Dog fence management holds concerns for the safety of sheep and cattle. ( Supplied: Katherine Moseby )

Dr Moseby owns a property she has turned into a nature reserve south of the fence on Eyre Peninsula, and accepts controls are needed on sheep grazing country.

However, she is concerned about the impact the change in policy will have in the cattle country north of the fence, if aerial baiting is allowed there for the first time.

"If you drive around north of the fence now, and you drive around for long enough, you'll catch a glimpse of the dingo," she said.

"They're quite elusive but you'll probably see some, particularly in wet years.

"If we go ahead with these types of changes, the dingo is going to become very rare north of the fence.

"We're going to see less and less of them and in some places they might become functionally extinct."

"Functional extinction" refers to a situation in which a species declines to the extent that it no longer has a role in the ecosystem, and may eventually die out.

Dr Moseby is also concerned about minimum baiting standards south of the fence, which will mean landholders will have to put out baits even if they have not seen evidence of dogs on their properties.

Pastoralists 'lying awake' fearful of wild dog impact

But the industry believes a broad approach is needed.

Dog Fence Board chairman and Mid North sheep farmer Geoff Power said dog populations are progressively moving south, and he and his neighbours are seeing the impact.

Geoff Power at his farm in Orroroo. ( Supplied: Miranda Kenny, AgCommunicators. )

"They can kill 30 or 40 sheep a night and those that they don't kill, you have to destroy because they're predated so badly that they wouldn't live and it's a real animal welfare problem," he said.

"I know one guy who had close to 2,000 sheep on one property and he only crutched 150 six months later, so it's just not sustainable."

It is stories like those that SA Agriculture Minister Tim Whetstone said he and Premier Steven Marshall heard when touring the state, consulting with farmers about the impact of the drought.

"That's why we've not got the boundary scheme in place that sits along other management tools," Mr Whetstone said.

"[We want to] support those pastoralists and those livestock producers who are lying awake in bed most nights wondering just how many stock they're going to lose due to wild dogs."

An industry leader says wild dogs can kill 30 to 40 sheep a night. ( Supplied: Invasive Animals Cooperative Research Centre )

While there is broad support for dingo control in South Australia's livestock industry, western Queensland grazier Angus Emmott said there was a different way to approach the problem, particularly north of the fence.

He has not killed a dingo on his property for a decade, and said the estimated 20 or 30 dogs on his property help control feral animals and kangaroo populations.

"Dingoes and sheep do not get along, dingoes and goats do not get along, but in straight cattle country, I find just leaving dingoes alone has a whole multitude of benefits," Mr Emmott said.

"You will lose an odd calf — but dingo family groups, when left alone, tend to not predate calves and chase things around the way that happens when you have persecution in the system.

"When you have persecution in the system, what actually happens is the family structure is broken down and you get packs of young dogs and they chase stock around for fun and will kill calves."

Ecologist calls for 'right balance'

Dr Moseby said Mr Emmott's example shows while controls are sometimes needed, they should only be implemented when there was scientific evidence of a problem.

A dingo pup in outback South Australia. ( Supplied: Katherine Moseby )

"Sometimes we do need to control dingoes to protect stock but a lot of the times we don't," she said.

"We need to make sure we get the balance right and there's nothing in that policy that gives me any assurance that we're going to have the balance right."

Mr Whetstone said the Government has been consulting widely, and would take into account concerns about the impact baiting would have north of the fence, along with exemptions for organic farmers.

"We think we've got the mix right with not only the bounty, the fence, the baiting program and the doggers out there," Mr Whetstone said.

"[We want to] sure we can do everything that should be done in supporting what should be one of our shining lights — the $4.3 billion livestock industry here in South Australia."

Consultation on the State Government's proposed changes has closed, with the final policy announcement expected later in the year.