The pro-brumby Snowy Mountains Bush Users Group filed legal action against Environment Minister Penny Sharpe in the NSW Supreme Court in June in a bid to stop the aerial killing, which was approved in October 2023.
The government aims to reduce the horse population to 3000 by mid-2027.
After a three-day hearing in July, Justice David Davies handed down his judgment on Wednesday and dismissed the case.
A judge has rejected claims Penny Sharpe made jurisdictional errors by allowing the brumby culling. (Mick Tsikas/AAP PHOTOS)
He rejected claims Ms Sharpe made jurisdictional errors by allowing the culling based on incomplete or misleading information.
The minister followed the correct procedures in making her decision, taking into account factors such as reducing wild-horse populations, minimising their environmental impacts and integrating this with the aerial shooting of other invasive species, the judge said.
"In circumstances where animal welfare considerations were but one factor to be considered ... I do not consider that the minister's decision was made other than on the basis of relevant and sufficient information," Justice Davies said.
The aerial shooting was only one of a host of measures to reduce brumby populations and it was not Ms Sharpe's duty to decide precisely how or where the helicopters were deployed, he said.
Justice Davies noted an animal-welfare assessment had been carried out by the RSPCA, which found laws preventing cruelty to animals had been complied with.
The judge ordered the group pay the government's legal costs of defending the case.
Invasive Species Council advocacy director Jack Gough said he was pleased the removal of feral horses would continue and expressed confidence it would be done professionally, safely and humanely.
He called the case a "deeply flawed legal challenge" by a small group that did not want to see a single horse removed from the park.
This lawsuit joined seven others in Victoria and NSW challenging brumby shooting that had been similarly thrown out, Mr Gough said.
"No one likes to see animals killed, but the sad reality is that we have a choice to make between urgently reducing the numbers of feral horses or accepting the destruction of sensitive alpine ecosystems and habitats, and the decline and extinction of native animals," he said.
Greens MP Sue Higginson said the decision was a "strong judgment" in favour of aerial shooting of invasive species, but she called for the state to go further and eliminate all feral animals in Kosciuszko.
"It is time to face the facts that the law that protects the horses in Kosciuszko was made on very dubious political grounds and should be repealed," she said.
Shooting operations were ordered to reduce horse numbers, which surged when rehoming was favoured under the previous coalition governments.
Prior counts showed there were more than 20,000 wild horses in the park, according to government estimates, posing a risk to the delicate alpine ecosystem.
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