"Humanitarian, military and diplomatic flights are not included in the ban," Talar Faiq Salih said.
Baghdad ordered the suspension of international flights from 6:00 pm (1500 GMT) Friday in retaliation for Iraqi Kurds voting for independence in a non-binding referendum earlier this week.
"I feel sorry for the situation we are in," Salih said. The civil aviation authority "is supposed to be independent... but in Iraq anyone can take a decision."
"It's a real punishment for Iraqis. They (Baghdad officials) should stop punishing their own people," she said.
Arbil airport is an international hub which has been used by humanitarian aid workers helping Iraqis affected by the battle against the Islamic State group.
The UN humanitarian office earlier said it was working to ensure aid could continue to reach tens of thousands of Iraqis in need, including those displaced by the battle for second city Mosul, which Iraqi forces retook from IS in July.
"OCHA is working with the authorities to ensure that humanitarian operations in Iraq can continue," it said.
"This includes coordination with the authorities on air travel for humanitarian workers into and out of Arbil," OCHA said in a statement.
,Humanitarian, military and diplomatic flights are not included in the ban,, Talar Faiq Salih said
Humanitarian, military and diplomatic planes are excluded from a ban on international flights to and from Iraqi Kurdistan to start on Friday, the director of Arbil airport said.
