The John Muir Trust (JMT), which campaigns for the protection of wild lands, had wanted to kill up to 100 deer in order to protect woodland habitats on its 9140-acre Quinag Estate, in north-west Sutherland, but Scottish Natural Heritage (SNH) rejected its application.
The JMT is particularly concerned at the impact of deer on Ardvar woodland, which is made up of ancient forestry and is protected under European and UK law.
However, landowners run sporting estates in the area and are dependent on the local deer population which belong to nobody. They had been particularly critical of JMT's plans and objected to such a big increase on the recommended cull levels.
The Assynt Crofters' Trust which acquired the 21,000 acres North Assynt Estate in a historic buy-out 20 years ago has also raised concerns about the cull.
Fraser Symonds, SNH's North Highlands and Islands operations manager, said consent to start the cull after February 15, the end of the hind season and before the stag season starts on July 1, had been refused. This was because JMT had already met its stag and hind cull targets, believed to be 45 and 80 respectively.
He conceded there was a problem at Ardvar woodland, from the pressure of deer which permitted culls had not solved.
Discussions with interested parties were under way on management measures to rectify this. However, SNH recognised a new plan of action was needed to address different and legitimate land management objectives. He said an aerial count of deer scheduled for early March would help guide future discussions.
However, Lester Standen, deer officer at the John Muir Trust, said: "We're disappointed and surprised SNH have refused the out-of-season authorisation for Quinag the Trust applied for, given they have already agreed we satisfy all the criteria.
"The Ardvar woodlands have been a designated Site of Special Scientific Interest since 1972, and a European Special Area of Conservation since 2005. Yet because the deer population in Ardvar has been allowed to triple this ancient woodland is in 'declining and unfavourable condition' according to SNH, and in danger of disappearing completely."
He added: "Sustainable deer management can bring many benefits in the form of local stalking income, venison in the food chain, native woodlands thriving naturally in Scotland for future generations without unsightly and ecologically damaging fences that cost taxpayers millions, and healthy deer able to access their natural woodland habitats when they need to."
He said the JMT would continue to try to persuade SNH and neighbouring land-owners this precious part of our country's rich natural heritage was worth protecting.