A dramatic plan to eradicate European carp from the Murray-Darling river system using a strain of the herpes virus may cause a pollution problem with dead fish littering waterways, a South Australian carp catcher has warned.

Key points: Federal Government project aims to eradicate 95 per cent of European carp

Federal Government project aims to eradicate 95 per cent of European carp Fisherman warns it will cause a huge pollution problem

Fisherman warns it will cause a huge pollution problem Tourism operators concerned it will affect business

Commercial carp fisherman Garry Warrick said his biggest fear over the plan was the prospect of water pollution from the dead pest.

"If the numbers of carp I know, which are around thousands of tonnes of them, if they died in quick succession, then there's going to be that many dead fish around there won't be enough people to clean it up," he said.

"I know the fish factory that I supply, they won't take dead carp.

"So I don't know what's going to happen to them."

Science Minister Christopher Pyne said the Government would find a use for the dead fish, with the prospect of turning them into pet food.

"We're going to either turn them into fertiliser, or pet food maybe, or dig enormous holes and put them in there," Mr Pyne said.

"But the decision's been made, the herpes virus can be released, and we'll get rid of these noxious pests."

Mr Warrick said the EPA did not allow large quantities of dead carp to be buried.

Yesterday the Government announced the $15 million project that would see a strain of the herpes virus, which was discovered in Israel, released into the river system by the end of 2018.

The virus only affects European carp and is expected to kill 95 per cent of the species of fish in the river system over the next 30 years.

Success rate of eradication questionable

Mr Warrick was sceptical the project would see the 95 per cent success rate as touted by the Federal Government.

He said the species' numbers in Israel had rebounded since the virus was released.

"It's a different environment, different water. It's untested and unproven at the moment," Mr Warrick said.

"Whether it works as it did in the laboratory, in the wild, we will have to wait and see."

He said the carp that survived the virus in Israel became immune to it.

"I did read they had a second strain ready to go if that does happen, or when it does happen," he said.

"If it works it will be a good thing for the environment."

Houseboat operator Robert Hughes was also concerned the dead carp could cause problems for tourism.

"I think a river full of dead carp is not going to be fantastic for business," he said.

Carp fertiliser company considers expansion

The director of fertiliser company Charlie Carp, Harold Clapham, said he would be able to put the many tonnes of dead carp to good use once the eradication program was rolled out.

"It won't damage the long-term prospects of our business — we think it will probably only enhance opportunities for our business," he said.

"There are a huge amount of logistical and practical issues that have to be dealt with [but] we can use dead carp."

Mr Clapham said there was a "genuine possibility" the New South Wales-based business would expand into South Australia, if the virus was released downstream.

"If the [kill] was to be somewhere along the River Murray system or somewhere in South Australia then we would [expand] because we source a huge amount of carp from South Australia already," he said.

"[The carp] basically have to be taken out within 24 hours or 48 hours of them dying because they can't be rotting.

"It's expensive to bring carp back from South Australia at the moment and if [the carp] were all dying down there, there would be a lot of sense in us moving down there ... we're not economic imbeciles."