"If you were a private operator on the Routeburn, you are prohibited from this behaviour - you've got no excuse for treating people differently," he said.
"It's clearly unlawful under the New Zealand Human Rights Act."
"[But] we realised the New Zealand Government basically has a carte-blanche get-out-of-jail free card - they can discriminate against non-citizens with absolute impunity.
Faulkner said the fact the Government had different rules under the Human Rights Act compared to everyone else was a cause for wider concern.
Having been born in New Zealand but lived in Australia since he was 6, Faulkner has been a long term advocate for the rights of Kiwis living across the Tasman.
He said that the Australian Government had been progressively introducing ever more discriminatory polices against Kiwis since 2001.
"I've been complaining bitterly for years about the poor protection against this form of discrimination that New Zealanders have in Australia," he said.
"[So] I'm very concerned when I see that lack of protection in New Zealand law.
"Once you start doing this type of thing, it tends to spread into other areas because Government departments see it as a way of saving money - that's what's happened over here in Australia to New Zealanders."
He said a country signing up to international treaties on human rights can decide who can vote in elections and who can enter their territory, but apart from that should treat everyone equally before the law.
DOC introduced the higher fees for foreigners using huts along four of New Zealand's nine Great Walks earlier this year as part of a seven month trial, running from October 2018 to April 2019.
They include huts along the Milford Track, Kepler, Routeburn and Abel Tasman Coastal Walk.
Conservation Minister Eugenie Sage said at the time the trial was designed to ease pressure on the walks from high visitor numbers and to help recoup an extra $2.9 million in revenue.
"The year ending March 2018 was another record year for visitor numbers to public conservation land with 1.75 million people, or 52 percent of all international tourists visiting a national park last year, up 5 percent, on the previous year," she said.
"International visitors currently make up around 60 percent of all those walking and using the Great Walks."
However, Faulkner said the fees not only violated international human rights treaties, but threatened to undermine New Zealand's tourism reputation.