This dispute centres on controls on farm land adjacent to trails created out of tenure review, which Federated Farmers claims the council's proposed district plan would treat differently from trails created by private negotiation or treaty.
The federation's South Island policy team leader, Matt Harcombe, said if the plan was adopted as proposed, trails created out of tenure review would be part of public place provisions, meaning any development on adjacent freehold land within view of the trails would be subject to resource consent.
Trails created out of private treaty would be exempt from public place provisions.
Given the importance of landscape protection in Queenstown Lakes, Mr Harcombe said public place provisions could become quite onerous for a developer.
But of more significance to the federation was the difference in treatment of land by the provision, known as plan change 28.
For example, two farmers wanting to build a haybarn in view of tracks - one created out of tenure review and the other by private treaty, would be treated quite differently because of the council's public place provisions.
"It creates two classes of public access in terms of assessment of public views," said Mr Harcombe.
The federation's immediate past Otago provincial president, Richard Burdon, said the proposal discriminated against one group of farmers.
"Why is this organisation targeting the high-country community?"Fresh from winning a High Court case against New Zealand Fish and Game and getting approval for their land stewardship from the Parliamentary Commissioner for the Environment, Mr Burdon said high country farmers were now having to fight this battle.
He warned the council's goal of a network of public trails could be compromised by farmers feeling threatened and not co-operating.
During tenure review, farmers might insist trails go through gullies and valleys, rather than up ridge lines, while private landowners might decide not to provide access, Mr Burdon said.
"The angle they are heading down doesn't provide winners or resolve the issue."
Queenstown District Council senior policy analyst Daniel Wells said creating trails was a priority for the council, but too few landowners were providing them.
During the plan's submission process, the council decided trails formed out of tenure review would be a public place.
Mr Wells said because farmers had gone through the tenure review process and, as part of that, set aside trails and access, the council decided no further incentive was required to encourage the provision of trails.
"We have not introduced any new landscape protection or taken away any development rights. The debate is about development rights that need to be conceded."
It was also about balancing landscape protection and public access, he said.