"The Civil Aviation Authority decided to suspend all departing and arriving flights from and to Arbil and Sulaimaniyah airports" for 48 hours from 8:00 am (0500 GMT) on today, it said in a statement, referring to airports in the autonomous Kurdish region.
The decision was made to "protect passengers and because of the crossing of cruise missiles and bombers from the northern part of Iraq to Syria, launched from the Caspian Sea and Iran and Iraq," it said.
In its bombing campaign, Moscow has twice fired salvoes of cruise missiles from warships in the Caspian Sea that passed over northern Iraq en route to their targets in Syria, most recently on Friday.
On Saturday, flights in and out of Lebanon were rerouted and some airlines cancelled services after Moscow requested they avoid an area over the eastern Mediterranean.
A US-led coalition is also carrying out strikes against IS in Iraq and Syria, where the jihadist group has declared a cross-border "caliphate" spanning territory it controls in the two countries.