The ban began at 6 pm (1500 GMT) at the airports of Kurdistan's capital Erbil and its second city of Sulaimaniya, according to independent Iraqi portal Alsumaria News.
Baghdad gave Kurdistan until Friday evening to hand over control of its airports or face a flight ban, a demand rejected by the territory's government.
The ban is part of measures taken by Baghdad in reaction to Kurdistan's unilateral vote on independence held on Monday.
A picture taken on September 29, 2017 shows empty check-in area at Ataturk International airport in Istanbul. AFP
A flight ban on Iraq's Kurdistan, imposed by the central government in Baghdad, has gone into effect at the autonomous region's airports.
