The NSW Parliament passed legislation on Wednesday that banned lethal culling of wild horses in Kosciuszko National Park, outraging scientists and environmental groups as the state government reversed a plan to cull an estimated 90 per cent of brumbies in the park over 20 years.

But brumbies that roam into the territory won't enjoy the same protection, with the ACT Parks and Conservation Service concerned about the impact they could have on Canberra's drinking water, as well as threatened plants and animals.

One of the capital's main water sources of drinking water, the Cotter catchment, is in the high country in Namadgi National Park.

ACT Parks and Conservation Service director Daniel Iglesias said feral horses would pose "quite a serious threat" to water quality if they got into the catchment.

"These animals will range right across the alps, and if we don't [euthanise them] and we let them come in, what will happen is quite predictable," Mr Iglesias said.

"We have some of the best water quality in the country, and that's because we've been able to keep feral animals out.

"The science is clear and there have been a lot of studies about the destructive impact [brumbies] have on water quality."

Mr Iglesias said traps had so far been very effective at keeping brumbies out of the territory, with no incidents in the past five years and no feral horses put down since 2007.

He said horse yards on this side of the border were used to trap brumbies, with a surveillance system in place to alert rangers when a horse was inside.

Brumbies that were caught in the traps were euthanised by a vet, he said.

"What we need to make clear is there are implications [from the new legislation] outside NSW," Mr Iglesias said.

"It's likely we will have more feral animals putting pressure on our border."

ACT Minister for the Environment and Heritage Mick Gentleman said he would be writing to the NSW government to express his concerns about the "reckless and irresponsible" legislation.

He said he was worried that failure to effectively control brumby numbers in Kosciuszko National Park posed a potential threat to the integrity of the Cotter catchment, and the sensitive sub-alpine environment in Namadgi National Park.

NSW Deputy Premier John Barilaro, who introduced the legislation protecting into the NSW Parliament, has said brumbies found in highly sensitive alpine areas of Kosciuszko National Park will be moved on.

"Resources will be allocated towards relocation first, followed by re-homing, should population numbers grow too high," he said, arguing that the Kosciuszko Wild Horse Heritage Bill 2018 struck the right balance between protecting "culturally significant" brumbies and the park's unique environment.

Brumby advocates including former Nationals MP Peter Cochran and Snowy Mountains Horse Riding Association spokeswoman Leisa Caldwell, who have welcomed the new legislation, have also said they have no issue with brumbies being relocated from alpine areas.