Last year, Turkey turned the Byzantine-era Hagia Sophia cathedral into a mosque for the first time since 1934.
UNESCO's World Heritage Committee asked Turkey on Friday to submit by early next year a report about the state of conservation of the Hagia Sophia, expressing "grave concern" over the consequences of its conversion into a mosque.
It said it "deeply regrets the lack of dialogue and information" over the change in status of the two shrines.
The Turkish foreign ministry said it "rejects the relevant articles of the UNESCO World Heritage Committee's decisions on Istanbul's historical sites understood to be driven by prejudiced, biased and political motives".
Hagia Sophia and Chora were state property and were being protected "meticulously," it said, accusing the UN of infringing on Turkish sovereignty.