The Department ordered Egyptian airlines on Wednesday to avoid Iranian airspace the following day after a message from Tehran about avoiding the airspace due to military exercises.
According to Egypt, the warning came in a message sent by Iran to all commercial airlines.
The warning comes amid increased tensions in the region since the politically labeled terrorist Hamas leader Ismail Haniya was killed in Iran last week – an act they accuse Israel of.
The ban applies for three hours, from 4:30 to 7:30 local time.
The head of Iran's international airport in Tehran earlier denied that a warning had been issued for the western airspace, but it is unclear whether it applied to the entire airspace, according to the state-controlled Iranian news agency Isna.
The escalation in the region has led many international airlines to cancel flights to Lebanon, Iran, and Israel.