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"The information summarised in this document is clear and unambiguous - feral horses have a litany of negative effects on native plants, animals and ecological communities," Professor Watson said in the letter.

The government justified the protection of brumbies, saying the animals' presence in alpine regions dated back to early European settlement. Its own 2016 draft policy recommended it cut horses numbers in the park by 90 per cent over 20 years to about 600.

"It strikes the right balance between protecting the environment and the heritage value of the brumbies that have been in the area for nearly 200 years," Ms Upton said in a speech to parliament supporting the bill.

Professor Watson told Fairfax Media that science was increasingly being treated by state, federal and other governments as just "one opinion", with elected officials instead opting for "politically expedient" options.

Government scientists were increasingly being muzzled, including in the Office of Environment and Heritage, he said: "They can't speak to anyone in the media about [their work]".

Scientific bodies including the Australian Academy of Science and International Union for Conservation of Nature are among those to have appealed to the Berejiklian government advising against the bill that overrides other conservation values in the national park.

Penny Sharpe, Labor's environment spokeswoman, said Professor Watson's resignation was "a terrible blow for NSW”.

“Science is not a stakeholder group, the advice of our scientists is key to good policy and we ignore scientists at our peril," she said. “The bill should never have been progressed and it is an indictment on the Minister for the Environment and the entire government that it has.”

Mehreen Faruqi, the Greens' environment spokeswoman, said the government had "consistently and deliberately ignored the advice of scientists - over vested interests - when it comes to the environment whether its land clearing laws or this bizarre bill to destroy the Kosciuszko National Park".

“This government has completely lost the trust of the scientific community," Dr Faruqi said. "This will be very hard to gain back."

Fish at risk

More indications of the threat posed by horses in the fragile alpine regions emerged on Thursday, with researchers from the University of Canberra's Institute for Applied Ecology warning the critically endangered stocky galaxias fish faced extinction from trampling of their habitat.

The species is now confined to a single population in a three-kilometre section of a small headwater stream in the national park.

“Brumbies are very abundant in the small catchment where the stocky galaxias live, and they are eroding stream banks at their numerous creek crossings," Mark Lintermans, an associate professor at the institute, said in statement.

"This degradation means that sediment is now smothering the galaxias’ breeding and feeding habitats."

The fish "need clean rocky-bottomed streams to breed." he said. "They attach their eggs to the underside of rocks, with the eggs taking 30-40 days to hatch in the cold upland environment."