According to the International Council on Monuments and Sites (ICOMOS), a wave of new tower blocks will alter key views and 'reduce the values' of the internationally important site.
The organisation is particularly concerned about how the Foster and Partners' redevelopment of the Old Royal Infirmary site, also called the Quartermile, will affect the skyline - 'one of the city's greatest assets.'
A spokesperson said: 'The coherence and integrity of the World Heritage Site is closely linked to its skyline and to the inter-relationship of individual buildings.
'[We] consider that the protection of this skyline is thus a key part of sustaining values of the World Heritage Site.'
The body draws comparisons with how proposals for tall buildings in other cities - such as Cologne - have led to World Heritage Sites being put on the 'in-danger list.'
ICOMOS is also shocked that Edinburgh council has approved skyscraper schemes just months before findings from a review of the existing High Building Policy are due to be revealed.
A spokesperson said: 'It is surprising that permission for three new towers at the Old Royal Infirmary site was granted in advance of the conclusions of this study in the light of the apparent acknowledged need by the city council to stand back and consider how new buildings could be integrated into the city without compromising its skyline.'
It is not the first time concerns have been raised about threats to the city's World Heritage Status. Late last year Edinburgh World Heritage director Zoe Clark also spoke out about how new 'lumpy eyesores' could impact on the city's historic standing ( Heritage boss speaks out over 'threat' to Edinburgh).