Te Araroa is a 3000km trail from Cape Reinga at the top of the North Island to Bluff at the bottom of the South Island.
Just outside Invercargill, the track goes through a combination of Department of Conservation owned, public and private land, including privately owned, Mt Linton Station.
"One walker was heading south through the station and deliberately left the marked trail to take a short cut through an active logging site," trail manager Dan Radford said on social media.
"The second was caught crossing the station by bike to meet the other walker."
The pair were subsequently trespassed from Mt Linton Station after the incident on Wednesday.
Te Araroa Trust, the group which manages the national trail, said it supported the decision.
"These decisions were a result of failing to read, comprehend and respect the trail notes, which Te Araroa Trust provide to keep walkers safe," Radford said.
It was made worse by the nature of where they took the shortcut, he said.
"It is dangerous - statistically, logging and agriculture are two of the most dangerous workplaces in New Zealand, and both occur regularly along Te Araroa."
Trust executive director Matt Caldridge said it was very unlikely the shortcut was taken by accident.
The pair would have had to ignore warning signs, advice provided by the trust and gone off a marked trail, he said.
"The information is clearly laid out and in this case there is absolutely no excuse for what the walkers did."
Despite the unfortunate nature of the incident, it was an anomaly amongst walkers, he believed and could not recall another time when a walker on the Te Araroa trail had been trespassed.
"We had 3000 walkers on the trail last year and this season and so to have two trespassers - the first time we believe walkers have been trespassed, so its incredibly rare."
