A scientific adviser to the NSW Government has quit over its decision to protect feral horses in the Kosciuszko National Park, saying the move shows a "wilful disregard" for science that "diminishes our collective future".

Professor David Watson, an ecologist at Charles Sturt University, had been a member of the NSW Government's Threatened Species Scientific Committee since January 2015 and advised the Government on managing threatened plants and animals in the state.

On Wednesday, the Government passed the Kosciuszko Wild Horse Heritage Bill 2018, which gave protected status to feral horses, colloquially referred to as "brumbies", despite the committee advising against doing so.

Minister for the Environment Gabrielle Upton said the bill "struck the right balance between protecting the environment and the heritage value of the brumbies that have been in the area for nearly 200 years".

Professor Watson told the ABC he could not stand by the decision.

"To see the responsible minister endorse the bill — for crying out loud, are you even trying to pretend that you consider the advice that we give you?" he said.

"I can no longer in good conscience give my time to a system that is clearly broken."

In his formal resignation letter, posted to Twitter, Professor Watson said the evidence of the damage the horses cause in the National Park is "clear and unambiguous", saying "feral horse populations have a litany of negative effects on native plants, animals and ecological communities".

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"Put simply, feral horses are incompatible with protected area management, a point made repeatedly in the days leading up to yesterday's decision by the IUCN," he wrote.

The decision came under fire not just by conservation groups, but peak scientific bodies.

The Australian Academy of Science published an open letter to the Government, saying the move "places a priority on a single invasive species over many native species and ecosystems, some of which are found nowhere else in the world".

The letter continued: "It is incompatible with the principles that underpin Australia's world-leading protected area system, and with our commitments as a signatory to the Convention on Biological Diversity."

The International Union for the Conservation of Nature, which advises the United Nations on scientific matters, also wrote to Ms Upton ahead of the bill being passed, saying it would create "a disturbing precedent at both national and global levels".

Ms Upton's office declined to comment on the resignation.

A spokesperson for the NSW Office of Environment and Heritage said: "David Watson's resignation has been accepted with regret.

"His knowledge and advice will be missed by those he worked with and his contribution to the Threatened Species Scientific Committee has been greatly valued."