The fishing industry in South Australia warns booming fur seal populations are threatening livelihoods by attacking their fishing nets and are preying on rare species and other birdlife, leaving rangers to put down pelicans in distress.

Coorong Wild Seafood owner Tracy Hill told 891 ABC Adelaide the seals were now seen in areas near the Murray mouth where they were not previously known.

"It's having an impact on the fishermen in the Coorong and the Lower Lakes, I can tell you that. We're going to be an endangered species ourselves if something can't be done about them," Ms Hill said.

"There's meant to be a 30-metre distance between seals and humans, well they haven't told the seals about that.

"They come right up to our boats, they can be just out of arm's length ripping our nets to pieces, because our nets in the Coorong and the Lakes are only six- and eight-ply nets. They're very thin nets."

She said historical data showed no evidence of seals in the Coorong or the freshwater lakes near the Murray mouth, and some had been seen in recent times attacking nets just south of Wellington, well upstream from the coast.

"The seals are attacking rare and endangered birds, such as the musk duck in the Coorong, and they're attacking pelicans, biting their legs off and attacking their wings," she said.

"Rangers have to go around and put down the pelicans in distress."

Other fishermen agree there is a threat to livelihoods.

Northern Zone Rock Lobster Fishermen's Association member Kyriakos Toumazos said New Zealand fur seals were taking over habitat around places such as Kangaroo Island, south of Adelaide.

"It's a species that basically takes over the habitat from the Australian sealion," he said.

"On Kangaroo Island the numbers of the Australian sealions are continuously declining due to the habitat takeover.

"The problem that I have is the extreme marine ecosystem damage they are doing and the Government is refusing to see the problem that lies in front of them."

Fur seals 'extremely aggressive', fishermen say

Mr Toumazos said the marine system was struggling because the fur seals were aggressive.

Lobster fishermen say the seals even attack their pots for a feed. ( ABC News: Andrew Fisher )

"The way we all have to view it is we have only one marine ecosystem and we are all harvesting fish out of that ecosystem. The seals obviously are competing for the same food source," he said.

"You've got a predator attacking as much of that fish source as it can get its hands on.

"They get into [lobster] pots, they pull fish out of nets, they're very clever and they know basically how to survive. They're extremely aggressive."

SA Department of Environment monitoring advisor Dr Brad Page said the Government was working with the fishing industry to come up with a solution other than culling.

"Some places in Tasmania have used firecrackers to scare seals away from fishing and aquaculture operations," he said.

"We're working with industry to look at how they can fish, how they can manage their fishing operations by tending their nets more and by reducing their soak times."

Family First MLC Robert Brokenshire said a Parliamentary inquiry had considered the problem.

"Some people have called for culling, now the reality is that we can't do that," he said.

"It would just damage our economy, it would ruin our tourism."

He said SA could not afford the bad reputation it would gain across the world if it culled.

Mr Brokenshire said officials had warned the fishing industry on Kangaroo Island of a bleak outlook.

"With the growth of the fur seal population, it's estimated within a few more years they will eat the equivalent of the whole of the Australian licensed fish catch per year," he said.

"Clearly they are knocking our fish stocks around and we've got a dilemma."

The Upper House MP said environment officials had argued with him and others that the fur seal population was only returning to levels it had before seals were harvested in a past era.

"They take the view that nature is actually just bringing it back into balance," Mr Brokenshire said.

"That's the argument they put to me, now I struggle with that and some of the people that work with penguins [protection] tell me they struggle with that."

SA Opposition Leader Steven Marshall said the Government had been slow to deal with the threats to both the fishing industry and environment.

"It's an area where the Government has just been burying its head in the sand, with other species as well," he said.

"It is a contentious issue and the Government needs to deal with it in a proactive way."

Mr Marshall said the Liberals were willing to work with the Government on responding effectively.