A virulent strain of herpes virus will be released into the Murray-Darling river system in a bid to eradicate European carp, in what Science Minister Christopher Pyne has dubbed a "carp-aggedon".

The Federal Government estimates the $15 million project will kill 95 per cent of carp in the river system over the next 30 years.

Speaking in Adelaide, Mr Pyne said the herpes strain cyprinid herpesvirus-3 would be released in 2018.

He said research by the CSIRO had shown the virus is safe, and has no impact on humans.

Mr Pyne said there will be "hundreds of thousands, if not millions of tonnes of carp" dead in the Murray River. ( ABC News: Martin Davies )

"It affects the European carp by attacking their kidneys, their skin, their gills and stopping them breathing effectively," he said.

"They have the virus for a week before they show any symptoms and it suddenly kills them within 24 hours."

He said the delay in release was due to the significant planning needed to deal with the sudden impact the virus may have on the river.

"Suddenly, there will be literally hundreds of thousands, if not millions of tonnes of carp that will be dead in the River Murray," Mr Pyne said.

"We have to have a clean-up program. We need a community consultation program. We need to have legislative changes potentially."

He said much of the $15 million in funding would go towards the disposal of the dead carp.

"There's obvious talk about whether the carp could be used for fertiliser, whether they could be used for pet food, whether they'll need to be buried in large graves and be allowed to dissipate back into the system," he said.

Joyce says carp the 'rabbits of our waterways'

Barnaby Joyce likened the carp to rabbits. ( Supplied )

Agriculture and Water Resources Minister Barnaby Joyce described European carp as the "rabbits of our waterways" and said the virus had a high success rate.

"We know even in conditions that don't quite work in our favour, we can have a kill rate of over 70 per cent," he said.

"We're looking at more than 500,000 tonnes of carp that will be killed, up to 2,000,000 tonne of carp.

"We've seen in lakes, in Japan, lakes that are multiple times the size of Sydney Harbour, we've lost 70 per cent of the European carp in two weeks."

He said damage caused by carp costs the economy as much as $500 million per year.

Scientists at the CSIRO have spent years testing the virus in "the world's most sophisticated high containment facility", to determine whether it can effectively reduce carp numbers without harming other species.

Carp were first introduced in the mid-1800s. ( Supplied: Marc Ainsworth )

"It causes high death rates in common carp and in the ornamental koi carp," the CSIRO website said.

"No other species of fish, including goldfish, are known to be affected by the virus."

Matt Barwick, a senior fisheries manager with the Department of Primary Industries, said people in Israel eat carp with traces of the virus every day, and there was no evidence of health issues.

"They treat almost all of their carp grown for human consumption with a live attenuated vaccine to this virus, which is basically a weakened version of the virus," he said.

"So there is up to 58 million individual carp that are eaten for breakfast in Israel every day, with this virus, and there's never been a single documented human health issue."

Carp were first introduced to Australia in the mid to late 1800s, and are now found in every Australian state outside the Northern Territory.

Widespread flooding in the 1970s helped spread the pests throughout the Murray-Darling system.