A major new review of how the government’s nature protection agency works has sparked warnings that the country's most precious wildlife is going to be put at risk in order to save money.

Environmental groups are worried that protection of the country’s 1,800 nature conservation areas - and the multitude of animals, trees and plants they contain - will now be diluted. This would be a mistake for which future generations would not forgive us, they say.

They fear that Scottish Natural Heritage (SNH) is bowing to the inevitability when it comes to future budget cuts, instead of fighting its corner for more money. SNH accepts that its review carries “significant risks” because of the opposition it will engender.

Among the many species of plants and animals at risk are puffins, harbour seals, fresh water pearl mussels and juniper. Areas where woodlands and plants could suffer include Loch Lomond, Ben Nevis, Glen Coe and the Cairngorms.

SNH has embarked on a major review of the way all protected wildlife areas, which cover 18 per cent of Scotland, are managed. It asked a panel of experts to produce some ideas, and it is now considering how to proceed.

A report to the SNH board in August suggested that the management of protected areas should be more “adaptive”. Global warming meant that some changes were inevitable, and would have to be accepted.

“It will be necessary to accommodate change by moving towards less prescriptive management which allows for a range of possible outcomes,” it said. “Under these circumstances management would tend to default towards minimum intervention”.

The SNH report admitted that the review had prompted concerns that it was “underpinned by cost-cutting or deregulatory agendas”. It added: “There are significant risks associated with this project, due primarily to potential adverse reactions from some stakeholders.”

In its initial response to the SNH review, the Royal Society for the Protection of Birds (RSPB) in Scotland was scathing. “Progressing with any one of these dilutions of the protected area system would be a mistake,” it said.

“The proposals are neither evidence-based nor logical. If read in isolation and implemented without wider analysis, they constitute a threat to the most treasured elements of the Scottish natural heritage and, unchallenged, they would undermine future efficacy of biodiversity conservation in Scotland.”

RSPB’s response also criticised SNH for failing to fight budget cuts. “We would rather see SNH make a stronger case for nature in the face of austerity than lower their ambition,” it said.

According to RSPB Scotland’s head of planning, Aedán Smith, the purpose of the SNH review was “a mystery”. The Scottish Government would not want to dilute protection for the best places for wildlife in Scotland, he argued.

“We are currently in challenging economic times but a high quality natural environment will be critical to the economic recovery of the nation, and provide an invaluable building block in shaping Scotland’s future,” he said.

“We need to concentrate on highlighting the fundamental importance of these amazing places to Scotland, now and in the future, and use the limited resources at our disposal on better implementation of our existing protected areas network.”

Dr Deborah Long, wildlife convenor of the umbrella group, Scottish Environment Link, and head of Plantlife Scotland, warned SNH not to go down a route that pushed nature to the margins.

She said: “Future generations will thank us for continuing to conserve today’s nature and in making space for it to thrive and become more resilient in the face on environmental change. They won’t thank us if we give up on conservation now.”

Head of policy for the Scottish Wildlife Trust, Dr Maggie Keegan, described protected areas as the “jewels in the crown” of Scotland’s natural heritage. “Whatever the outcome of SNH’s review, the biodiversity value of these sites must not be diminished,” she said.

SNH pointed out that there were limits to what protected areas could achieve in the face of pollution, rising sea levels, and growing levels of consumption. There was a need for a willingness to consider new approaches, it suggested.

“Protected areas for nature have been an essential tool in nature conservation and the management of our countryside for 60 years,” SNH policy director, Andrew Bachell, told the Sunday Herald.

“These areas will always play a key role in our conservation approach. However, in the face of climate change, changes in land use and growing interest in how nature supports tourism, health and other benefits it is always important to make sure that we consider the wider role played by protected areas.”

He added: “Through this review our aim is to better understand how we can all work together to tackle the challenges that Scotland’s nature will face in the coming decades.”