The government’s wildlife agency, Scottish Natural Heritage (SNH), has come under fire after backing down on a plan to take legal action against landowners who don’t kill enough deer to protect ancient woodlands.

Environmentalists say that excessive numbers of deer are damaging native forests by eating saplings and preventing natural regeneration. But sporting estates rely on the deer to earn income from shooting parties.

The clash, which has long plagued nature conservation arguments in Scotland, has come to a head on the Assynt peninsula in the far northwest highlands. The area has three major landowners and a population of red deer variously estimated at between 800 and 1,800.

According to SNH, the deer are harming an important birch woodland at Ardvar, designated as a protected nature conservation area. The woodland has been classified as being in an “unfavourable declining” condition since 2004.

A series of voluntary agreements with the landowners have failed to solve the problem, SNH says. Some of the owners, including the Assynt Crofters Trust, run deer stalking businesses.

Under pressure from the Scottish Government to act, the SNH board decided in June to take the unprecedented step of initiating legal action to curb deer populations. It threatened to step in and shoot deer itself, if landowners failed to.

But this prompted a storm of protest from the Assynt crofters, who fiercely disputed SNH’s estimates of deer numbers and its understanding of the Ardvar woodlands. They said they would be prepared to go to prison to defend their rights as landowners.

Documents released under freedom of information law reveal that the protests forced SNH to back down. It is now negotiating another voluntary deer management agreement with the landowners instead of pursuing legal action.

In an email in on 2 August SNH’s director of operations, Nick Halfhide, accepted that his new discussions with landowners would be “unsettling” for disgruntled staff who had spent months preparing for legal action.

In an internal memo on 25 August, he explained that he was attempting to “normalise our approach at Assynt” by negotiating a voluntary agreement.

He wrote: “Are we going soft? Not at all. This is a pragmatic solution to a situation that was threatening to soak up vast amounts of time and lead to more personal attacks on staff.”

But his move has been criticised by environmental groups. They pointed out that SNH had been asked by the Scottish Government to use its statutory powers to manage deer populations in the public interest.

“The Ardvar decision appears outwardly inconsistent,” said Duncan Orr-Ewing, who chairs the deer task force for the umbrella group, Scottish Environment Link. “It may set an adverse precedent in relation to the firm action needed to tackle deer damage to wildlife habitats elsewhere in Scotland.”

The John Muir Trust, a wild land conservation group that owns land at Assynt, has been involved in the discussions with SNH and other landowners. “We are working hard to make the current voluntary plan work,” said the trust’s head of land management, Mike Daniels.

But he argued that the powers that SNH had under deer legislation weren’t fit for purpose. “Neither they, nor the voluntary plan can deliver everyone’s aims,” he said.

“Instead, we are very much in favour of smarter, simpler and stronger regulation of deer management in Scotland.”

The Assynt Crofters Trust welcomed the shift in SNH’s position. “We have been pushing SNH for an explanation of their change of direction and a statement to the effect that they mismanaged the Ardvar situation over a number of years,” said the trust’s vice-chair, Ray Mackay.

He pointed out there was “nothing to stop SNH doing another volte-face and re-igniting this whole issue”. There was something “fundamentally wrong” with the way SNH was run, he alleged.

“It is not at all obvious what function, other than being a rubber stamp, the board serves, whether there are sufficient checks on the power of certain officials and, finally, whether SNH is actually fit for purpose.”

He was backed by woodland consultant, Victor Clements, who is also involved in the negotiations with SNH. “They have developed a blindness to the regeneration that exists in Assynt,” he said.

“Many SNH personnel have allowed themselves to become too closely aligned with environmental groups, and have, consciously or unconsciously, taken on their agendas.”

Clements thought that SNH had been humiliated and needed to be restructured. “This process has flagged up a very serious deficiency in governance that we should all be concerned about,” he said.

SNH stressed that the deer management agreement was still under discussion and nothing was finalised. “We want to see the beautiful woodlands in Assynt flourish and we’re close to an agreement with the local estates to achieve this,” Halfhide told The Ferret.

“We’re making good progress throughout Scotland to ensure that wild deer are managed sustainably and in balance with the environment. We will use all our powers, including compulsory legal orders when necessary, to achieve this.”

A version of this story was published in the Sunday Herald on 17 December 2017.