The move comes after concerns were raised by delegates over the handling of the controversial Caltongate development in the city's Old Town.
Unesco rules state that the government must consult it on any major developments in a heritage site before approval is granted.
However the Scottish Government approved the scheme last month after dismissing demands for a public inquiry, 1,800 objections and failing to consult Unesco before coming to a final decision on the scheme, which will see two listed buildings demolished to make way for a five-star hotel.
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The development plans also include an office complex and 200 homes.
The Scottish Government has been given until February 2009 to defend the capital's status. Delegates at Seville's 2009 Unesco summit will decide if the city has broken the rules.
Dr Mechtild Rossler, head of the European Unit for the Unesco World Heritage Centre, told BBC Scotland: "We have a number of concerns about some new developments in the Canongate area, Leith docks, St James Centre and the Cowgate fire site.
"We have informed the World Heritage committee about these developments and expressed concern and that's why the committee requested that the state party invite a mission to the site.
"We are concerned about potential impact on the outstanding universal value of World Heritage property."
Culture Minister Linda Fabiani said: "I'm confident that when the Unesco mission visits our capital, it will see a vibrant, growing city which embraces its cultural and architectural heritage as well as managing an improvement in development that benefits Edinburgh as a whole."
(GK/JM)
