It follows reports that the world heritage body is calling for information on the impact of the hotels amid concerns that some of the city’s famous views are being disrupted.
The probe is understood to stem from plans to build a 12-storey ‘ribbon’ shaped hotel as part of the new £850m Edinburgh St James development and a bid to turn the city’s historic Royal High School building in to a £75m luxury hotel.
Inspectors from the International Council on Monuments and Sites (Icomos), which advises UNESCO, descended on the city in October to assess the impact of the developments.
Now the UK and Scottish Governments are being questioned over the managing of the world heritage city after inspectors warned that the ‘potentially negative' impact of the new developments was becoming 'increasingly apparent'.
Edinburgh City Council has also been asked to explain its stewardship of the site.
Ian Perry, the council’s planning leader, told The Scotsman: “The present and past planning committees have had a duty to maintain the world heritage site. However there is always a tension between the desire to develop within the site and the preservation of its architectural heritage. Clearly there are differing views about how this should be interpreted.
“It is the planning committee’s job to try to allow development to happen without damaging the built heritage of Edinburgh, which in the past has proven difficult and some of the developments have obviously been controversial.
“The present planning committee will now be looking at the management of the world heritage site and will review what has happened in the past.
“If we think there needs to be changes we will then consult the Edinburgh World Heritage Trust.”
In August Councillors ignored concerns from their own officials to approve construction of the 210-room ‘ribbon’ hotel – dubbed a 'walnut whip' and #theturd by its critics.
This was despite planning officials warning that the hotel would ‘damage’ the city skyline and that the its bronze stainless steel coating was ‘too shiny and reflective’.
Plans to turn Edinburgh’s Royal High School building in to a £75m five-star hotel were rejected in December.
But Urbanist Hotels – which was behind the development – insisted its contract with the council would last until 2022, giving developers seven years to lodge a new planning application.
A spokesperson for the Scottish government said they were 'considering' UNESCO's concerns and would be advising the Department for Culture, Media and Sport over the issue.
In 2009 UNESCO dropped Dresden from its list of World Heritage Sites for building a 1.8km bridge outside the city.