The spectacular dunes system picked by Donald Trump for his golf resort in Aberdeenshire has been “partially destroyed” as a result of the course’s construction, documents released under the Freedom of Information Act have revealed.

Scottish Natural Heritage, which has been under pressure for years to speak out on the issue, now acknowledges that serious damage has been done to the site of special scientific interest (SSSI) at Foveran Links on the Menie estate, north of Aberdeen, since the course opened in 2012, the documents show.

As a result, Foveran’s SSSI status – given because of its unusual shifting sands and diverse plant life – now hangs in the balance.

“Construction of the new golf course involved earthworks, planting of trees, greens and fairways, drainage, irrigation and grass planting,” states one of the reports released by Scottish Natural Heritage inspectors. “This has affected the natural morphology of the dunes and interfered with natural processes. Most of its important geomorphological features have been lost or reduced to fragments. Nearby marine terraces have also been reduced to fragments.”

Bob Ward, the policy director at the Grantham Research Institute on Climate Change and the Environment, said: “These documents show that considerable damage has been done to Foveran Links, and that it is very unlikely that it will retain its SSSI status.”

Ward, who obtained the reports under FoI, has also asked the Scottish government to investigate whether proper environmental monitoring has been carried out at the site since 2012.

Facebook Twitter Pinterest The clubhouse on the Menie estate, rebranded Trump Aberdeen. Photograph: Murdo Macleod/The Guardian

A decision to remove the scientific status of the links could affect the US president’s recently announced plans to invest a further £150m in the resort.

Scottish Natural Heritage has been reviewing the state of the lengthy stretch of mobile dunes partly covered by the course for several years and had promised to publish its findings late last year. However, the group has still to outline its views in public.

Trump originally won approval for his “Trump Estate” encompassing the protected dunes because he pledged to create up to 6,000 jobs by building a five-star hotel with 450 rooms, shops, a sports complex, timeshare flats, two golf courses and housing estates there. However, so far he has constructed only one 18-hole course, which is open seven months a year, a practice range, and a small clubhouse with a restaurant and shop; he also converted Menie’s manor house into a boutique hotel with 16 rooms.

Many local residents and councillors believe that the development did not justify destroying the delicate ecosystem at Foveran. They say Trump failed to honour promises he made in 2008 to protect the site as much as possible when he encouraged a planning inquiry to ignore the dunes’ SSSI status.

Normally the site’s conservation status would have prevented any significant development. But Trump said that, if he was refused permission to develop on the southern end of the SSSI, he would withdraw from the entire scheme. He also claimed that, when completed, the land there would be “environmentally enhanced and better than it was before”. The Trump Organization said last year its environmental approach to the course had been “first class”.

That view is disputed by conservationists. “It’s been ruined from a virgin, undeveloped wilderness site into something that’s relatively manicured,” said Dr Jim Hansom, a specialist in coastal ecology at Glasgow University. He told a recent BBC Scotland documentary the site had lost the key features that led to it being given protection. The decision to approve the course was met with anger by conservation groups. “It appears that the desires of one high-profile overseas developer, who refused to compromise one inch, have been allowed to override the legal protection of this important site. And we fear this sets a precedent that will undermine the whole protected-sites network in Scotland,” Aedán Smith, head of planning and development at RSPB Scotland, told the Times.

Trump – whose visit to his other Scottish golf course at Turnberry this month triggered protests – infuriated conservationists in the US this month by proposing to weaken the landmark law that saved the bald eagle, the wolf and other species from extinction.