A delicate ecosystem of shifting sand dunes has been “reduced to fragments” by the construction of Donald Trump’s Aberdeenshire golf course, according to a previously secret report, which suggests its designation as a site of special scientific interest (SSSI) is at risk as a result.

The Foveran Links Site of Special Scientific Interest (SSSI) was partially destroyed by the Trump International Golf Links on the Menie estate, documents released by Scottish Natural Heritage (SNH) under Freedom of Information laws revealed.

The back nine holes of the course lies within the Menie section of the SSSI, which covers about a third of the total area.

Changes necessary for the course have disrupted natural processes and stopped the movement of the dunes, the report, penned in 2016, found.

“Construction of the new golf course involved earthworks, planting of trees, greens and fairways, drainage, irrigation and dune stabilisation [including] marram grass planting in combination with chestnut pale fencing and seeding/re-seeding," it said. "This has affected the natural morphology of Menie’s dunes and interfered with natural processes. Most of its important geomorphological features have been lost or reduced to fragments.

“In particular, the Menie sand sheet has been stabilised, part of the Sandend burn sheet has been lost, and nearby slacks and emerged marine terrace have been reduced to fragments.”

The report concluded: “In summary, part of the site has been destroyed or damaged by the construction of the golf course on Menie.”

The SSSI's boundaries are now being considered as part of a wider review by Scottish National Heritage.

Trump International defended the Menie development, saying its environmental methodology had been “commended” during construction.

Mr Trump’s developments in Scotland have attracted significant protest before, during and after their construction.

Most recently, during the US president’s visit to the UK, a protester in a powered parachute was able to breach a no-fly zone around his Turnberry resort to display a “Trump well below par” banner despite heightened security.

Prior to the arrival of the Trump Aberdeen resort the wider Foveran Links site was “probably one of the least disturbed and most dynamic sand dune systems in Britain”, the 2016 report said.

It supported a number of rare or declining plants within a “remarkable collection of landforms and habitats”, the report added, but “it is likely that at least some of these habitats will not continue to exist in their current form in the foreseeable future”.

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SNH admitted the site’s inclusion within the SSSI designation was now at risk. Emails and other notes also released under Freedom of Information rules suggested denotifiying only part of the SSSI was possible.

Ross Johnston, the group’s head of operations, said: “We are reviewing a number of SSSI designations across Scotland including the Foveran Links SSSI which overlaps the Menie golf course. In response to a request for information, we have released the site condition monitoring report that has been prepared as part of the review.

“The results of the full review will be published after it has been considered by SNH’s board later in the year.”

It comes just days after the Trump Organisation announced it would seek permission to build 500 houses, 50 cottages, a sports centre, a shopping centre and a horse riding facility at the Menie estate in a £150m expansion.

The company, now run by the president’s sons Donald Jr and Eric, claimed the latest phase would support nearly 2,000 jobs across Aberdeen and Aberdeenshire during construction, and provide nearly 300 permanent jobs.

Sarah Malone, the executive vice president of Trump International, said in a statement to The Independent: ”Trump International owns less than 5 per cent of the SSSI; 95 per cent lies north of our site and remains completely untouched.

“As for the small portion that we do own, no other SSSI site in the land has seen more environmental care or investment. The site was ignored until Trump took ownership and is now celebrated and enjoyed by many.

“As for the geomorphic component of the land that occupies our golf course, it is less than 4 per cent of the entire SSSI site and, of course, it has changed in parts because we have sown grass but our environmental consultants and SNH can confirm that many of the special attributes of the land remains and the wildlife is flourishing.