Turkish Foreign Minister Mevlut Cavusoglu said the Kirkuk provincial assembly's decision "will not help Iraq's future, stability and security."
Turkey expressed concerns on Wednesday over the decision of an Iraqi provincial assembly to raise the Kurdish flag alongside the Iraqi national flag at public buildings.
On Tuesday, 26 Kurdish members of Kirkuk's provincial assembly voted in favour of raising the Kurdish flag alongside Iraq's national flag at the city's public buildings and institutions.
"We don't approve of this voting held by the regional administration," Turkish Foreign Minister Mevlut Cavusoglu said in an interview with state-broadcaster TRT Haber.
TRT World spoke to Owen Holdaway who has more from Erbil.
The United Nations Assistance Mission for Iraq (UNAMI) also said it was concerned by the recent decision of the governor of Kirkuk.
Iraqi Vice-President Osama al Nujeifi also condemned the move on Tuesday, saying it could lead to friction between Kirkuk residents.
There are nine Turkmen and six Arab representatives in the 41-member Kirkuk provincial council, who were conspicuously absent during Tuesday's vote.
Kirkuk's population is mainly composed of Arab, Turkmen and Kurdish inhabitants.
The city's Turkmen residents opposed this idea, saying Kirkuk should enjoy a "special status."