Pyne said past programmes introducing the virus in some Japanese lakes has resulted in 70 per cent of the carp dying within just a few weeks.
So what to do with all those dead fish?
"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," Pyne told the Australian Broadcasting Corporation.
He estimates that the dead carp mass will be between 500,000 and 2 million tonnes.
The virus will not affect the other fish in the river, and Matt Barwick, a senior fisheries manager with the Department of Primary Industries, said it also will not endanger the humans that might eat them.
However, the carp-killing initiative must be supplemented by efforts to support native fish species and promote river health, Jonathan La Nauze, healthy ecosystems programme manager for the Australian Conservation Foundation told the Guardian.
"The legacy of past mismanagement in the Murray-Darling is that 21 out of the 23 major river valleys are in poor or very poor health, according to the Sustainable Rivers Audit," La Nauze said.
Because carp are bottom-feeders, they stir up mud and sediment, turning rivers into "into muddy, soupy streams that sometimes fail to clear over a summer," according to Ken Smith, an angler who writes for Fishing World.
Pyne estimates the carp cost the Australian economy up to A$500 million annually.