The chair of the NSW Fisheries' scientific committee has resigned in protest after the state government approved the Snowy 2.0 main works, saying the move will likely result in an endangered fish becoming extinct.
Redfin are one of the major problems, with the scheme likely to transport the pest species into areas they are currently not occupying, putting at risk both native fish stocks as well as preferred holdings of economically important trout.
Deputy Premier John Barilaro on Thursday announced state planning approval for the project inside the Kosciuszko National Park, which involves the construction of a 240m long pumped-hydro power station about 800m underground.
The government claims the project will create 2000 jobs during the construction phase and generate billions of dollars of investment in regional NSW.
But Associate Professor Mark Lintermans, who has worked with the fisheries committee for nine years, said the state government didn't ask for formal advice before approving the energy project.
"We provided some advice but then got no response back," the committee chair told AAP on Friday.
Following a consultation process that sought submissions from the public, Lintermans said all government decisions were made "behind closed doors".
"It was a controversial topic, the pressure is immense to find alternative energy sources, and I assume this was the quickest way to do that," he said.
Lintermans is particularly worried about the critically endangered freshwater fish species the stocky galaxias and Macquarie perch that are native to the area.
"It's highly likely the stocky galaxias will go extinct in the wild and it may go extinct altogether," he said.
Lintermans is calling for an independent review of the project's long-term impact.
The state government said Snowy 2.0 will add 350-gigawatt hours of energy storage and 2000 megawatts of generation capacity to the state's grid - enough to power 500,000 homes during peak demand.
But National Parks Association of NSW executive officer Gary Dunnett said the decision sets a dangerous precedent as the large-scale industrial development is inside a national park.
"Australia has been an international leader in managing national parks," Dunnet told AAP on Friday.
"(But) here we are undermining it with the largest development ever proposed in a NSW national park.
"National parks should be about setting aside special places for future generations who deserve to inherit them in better condition than how they are now."
Planning Minister Rob Stokes said the project's approval included strict conditions and the investment of $100 million for biodiversity and environmental offsets to protect threatened species.
Dunnett argued there's no equivalent to leaving the land alone.