Dr Faruqi said "cruel methods such as aerial shooting are unacceptable", and called on the government to "finally invest in non-lethal and humane population control measures".

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Keith Muir, director of The Colong Foundation for Wilderness, told Dr Faruqi he was "puzzled" by the apparent opposition to culling horses, a stance that puts the Greens "firmly in the Nationals camp of rehoming and fertility control of feral horses".

"To be consistent, surely the Greens NSW would need to also support rehoming of foxes, rabbits, pigs and deer?" Mr Muir said.

Greens insiders were also angered.

One said Dr Faruqi had "mischaracterised" party policy, which specifically includes lethal methods of feral population controls. By making the Greens stance "very, very murky", it could leave open the door for the "really stupid policy" to get through.

"It's just ridiculous," another insider said. "The Greens can't be the environment party and sit on the fence when it comes to a serious environmental issue."

Dr Faruqi will soon join the Senate as the replacement for Lee Rhiannon who on Friday announced her retirement by mid-August. She downplayed friction with her colleagues.

“Greens policy has always been about managing invasive species humanely through non-lethal methods wherever possible, while ensuring that if lethal methods are to be used as a last resort, they are done humanely, through professional, effective and scientifically proven methods," she told Fairfax Media.

“I have been an environmentalist my whole life with a 25-year career in preserving the natural environment."

Tensions, while less evident, are simmering among Liberals.

Attorney-General Mark Speakman, a former environment minister who had backed the draft plan to reduce horse numbers by 90 per cent, "strongly opposes" the policy, a Liberal source said.

"As a member of cabinet, I support all cabinet decisions," Mr Speakman said when approached by Fairfax Media.

"There is certainly disquiet," one Liberal MP said.

"It's unhelpful when you go to a [News Corp] newspaper before the party room," the MP said, adding that an effort to have the new policy "reconsidered and re-presented" was dismissed.

In a speech to Parliament this week, Mr Barilaro said:

"If we accept that the brumby has a right to exist in the Snowy Mountains region — a right that this bill encapsulates — and we recognise the brumby's unique place in Australian history, then we must find ways to preserve a sustainable population in a way that minimises harm to the environment."