Scientists from the Threatened Species Recovery Hub found the effects of four pathogens, including Toxoplasma gondii and Sarcocystis gigantea, caused a range of animal health impacts, including spontaneous abortions, still births, neonatal deaths and visible cysts, in meat.

They found SA, particularly Kangaroo Island, and Tasmania, were the two Australian hotspots for the pathogens.

Leading Tasmanian veterinarian Bruce Jackson, formerly of the Department of Primary Industries, Parks, Water and Environment, estimated annual losses in Tasmania could now be as high as $2 million.

"I had a veterinary student who did a study on four properties that had outbreaks.

"Two of the properties had lost $70,000 worth of lambs, they had massive outbreaks," Mr Jackson said.

"Those properties were in northern Tasmania, but I am sure the problem is spread around."

He said surveys had shown that more than 80 per cent of feral cats were carriers of the toxoplasma pathogen, which caused abortions in sheep.

Losses were not usually as high from sarcocystis, as it usually involved trimming or condemnation of sheep and lamb carcases.

"We have seen nasty situations where a third of quite large lines of mutton have been condemned because of this," he said.

"With abortions, you lose the whole lamb."

The pathogens produce eggs, that are passed in cat faeces. The eggs persist in soil, pasture and water, and are subsequently ingested by stock.

"Everyone is aware of it - the big question is what to do about it, as the four big outbreaks the student did case studies on, all had quite strong cat control programs," Mr Jackson said.

"But it appeared one cat did wander across the paddocks and away it went.

"The individual cat only excretes for two weeks, but produces millions upon millions of eggs, one cat can do a lot of damage."

John Fowler runs sheep on the edge of the town of Bothwell, Tas.

"We were getting meat rejected by the abattoirs," Mr Fowler said.

"We used to have a hay barn, which had an awful lot of cats.

"We're not putting hay in the barn anymore.

"But the fact we were abutting the town meant we had lovely accommodation for them."

His son Russell Fowler was now largely running the family's four farms and 7000 breeding ewes.

He said he had had problems several years ago, estimating he lost 150 lambs in one season in a flood irrigated paddock on the edge of town.

From scanning, he estimated abortions in a flock of 350 mixed-age ewes ran at about 50pc.

"I got one of our workmen to have a crack at the cats in the barn and he got 47," he said.

"Abortions, they were, they were scanned in-lamb, and went into that paddock from then until lambing they aborted.

"It's a flood-irrigated paddock, so there was lots of grass around, so it was hard to see if there were foetuses."

At a cost of $90 a lamb, he estimated the loss to be $13,500.

"I'm starting to see a few more cats about, more than usual.

"I see one every now and again, on the side of the road.

"Any shooters we have on the property, we tell them to get cats if they see them, but they are not targeting them."

The researchers surveyed the incidence of Toxoplasmosis gondii in feral cats across Australia, using molecular analysis and cat tissue samples.

They found the gondii infection was more common in feral cats living in cooler, wetter areas, where oocysts (eggs) were likely to survive for longer in the environment

One of the researchers, University of Adelaide Adjunct Fellow and Wildlife Ecologist Dr Patrick Taggart said while Victoria and New South Wales had the largest sheep flocks, South Australia and Tasmania had higher rates of sarcocystosis infections.

"The main reason is that South Australia's figures are really driven by Kangaroo Island," Dr Taggart said.

"Kangaroo Island has a high density of cats, and so does Tasmania.

"We know on Kangaroo Island there are no wild dogs or dingoes, there are no foxes, and the same applies to Tasmania."

But he said the impact of the pathogens, particularly toxoplasmosis, could be quite difficult to detect and quantify, unlike fly strike, which was more obvious.

"It may be the farmer never knew that ewe was actually pregnant, and it's quite unlikely they would submit aborted foetuses for testing," he said.

While vaccines for toxoplasmosis were available in other countries, Australian farmers did not have access to them.

"At the core of it, it really comes back to effective and efficient cat management," he said.

"The egg phase of the parasite contaminates feed, water and soil.

"They are quite environmentally resistant, and they then get spread around by rain washing them around, or by the wind.

"The animals become infected by consuming the contaminated food, soil or water."