The Scottish natural heritage said that about one-third of the dunes on Menie Estate have been damaged in course development.
The remainder of the habitats in the area have been "substantially fragmented and ecological processes disturbed," the agency said.
The dune site covers about 154 hectares, or about 0.6 square kilometers. The development has damaged about 15% of the area and the conservation group removes the area from the Foveran Links site for particular scientific interest pending a three-month consultation.
"The delisting of SSSIs is unusual, but in this case we have found that there is no longer a reason to protect the dunes on Menie, as they do not contain enough of the particular natural properties that they was appointed, "says Sally Thomas, director of human and nature for Scottish natural heritage, in a Newsletter.
The site is a "very high quality example" of a sand dune system typical of northeast Scotland, said the agency, important for the wide variety of coastal landscapes and processes in the region.
The remaining feverish Links site will be merged with the adjacent Sands of Forvie and Ythan Estuary Site of Special Scientific Interest. The Scottish natural heritage said.
Trump Organization did not respond promptly to a request for comment. Trump owns two golf courses in Scotland: one in Aberdeen and another in Turnberry. The Aberdeen course, which was opened in 2012, has been received by opposition from locals and environmentalists.