A rapid kill of carp in the River Murray using a strain of the herpes virus could lead to big side effects for the health of the ecosystem, early research findings have shown.

The Federal Government is hoping to release cyprinid herpesvirus-3 at the end of 2018 to reduce huge numbers of the introduced pest.

The strain has been proven to kill carp without affecting other species.

Research is now underway to work out how the ecosystem would change without them, and with the decomposition of their bodies.

Small changes in oxygen levels can have big ramifications for native wildlife.

So researchers at the University of Adelaide have been putting dead carp into 800-litre tubs of water to try to measure the amount of oxygen the decomposing fish use up.

Although the work is in its early stages, researcher Richie Walsh said it was showing some dramatic results.

"We found that at 20 degrees, one carp can almost completely remove oxygen from the water in less than 48 hours," he said.

"There's a lot of things we need to determine, but so far my research does indicate that there will be huge side effects for the rest of the ecosystem."

If the herpes virus is released, there is the potential that millions of tonnes of rotting fish will have to be removed from the system.

Mr Walsh said there was evidence to suggest the carp might not float.

"A lot of them may sink, which will make removal obviously very difficult, even if we had the time and money to get them out," he said.

Carp-ageddon needs environmental approvals

Carp are often referred to as the rabbits of the river.

Since being introduced, the bottom feeders now make up more than 80 per cent of fish biomass in the Murray system and cost the economy an estimated $500 million each year from the damage they cause.

Matt Barwick from the New South Wales Department of Primary Industries, who is working on the project, said nothing would go ahead without a series of environmental and social approvals.

"We will need to have a very effective clean-up strategy in place to protect water quality both for human use and to protect our native species," he said.

"This is a fantastic opportunity, one of the biggest ecological interventions that we will have seen in our generation that will result in our waterways, the health of our waterways and fisheries transforming.

"If the risks that are borne out of the legislative approval process and the public consultation process can't be resolved, clearly this won't go ahead."

Mr Barwick said those involved were looking at international case studies, as well as undertaking new research.

SA won't rush to make a decision

Zane Skrypek, who fishes for native species of golden perch and brings in a by-catch of carp, said the pest was in abundance in the river to the detriment of native fish.

Fisherman Zane Skrypek fears the carp kill will also kill native species. ( ABC News: Nicola Gage )

"So majority of carp goes for southern rock lobster bait, some of it does go for human consumption, mainly interstate Sydney and Melbourne markets," he said.

"Through the warmer months where the carp are closer into shore the volume of them is astronomical. We are catching anywhere between 800 and a tonne a day of carp. So a lot of fish."

He added

That volume of fish dying to clean up is impossible.

"My concerns are the water quality. When you have that amount of fish dying, the oxygen levels are going to be removed.

"No oxygen in the water means other species will be killed, so your native fish."

Fisherman Garry Hera-Singh has questioned whether removing so many dead fish was realistic.

He said the process should not be rushed and wanted other removal options to also be explored.

"The original proposal about using genetics over a longer timeframe was a smart move," he said.

Communities could also be called on to help with the clean-up if the proposal goes ahead.

National strategy needed: Biosecurity SA

Biosecurity SA said further research was needed to develop a "comprehensive national release strategy that would minimise potential risks to water quality".

"The [SA] Government will not be rushing into a decision to support the national release without comprehensive scientific information regarding the host specificity of the virus and the environmental risks of a mass carp die-off," it said in a statement.

The Federal Government has committed $15 million to the project.