“At the request of the central government of Iraq, all flights from Iran to Sulaymaniyah and Irbil, as well as all flights through our airspace originating from the Kurdistan region, have been stopped,” said Supreme National Security Council spokesman Keivan Khosravi, according to official news agency IRNA.
The move was due to “the insistence” of Kurdistan officials in holding the referendum, Khosravi said.
He did not specify how long the ban would stay in place.
The vote was set to go ahead Monday despite opposition from Baghdad and its neighbors, including Tehran.
Iran warned last week that independence for the region would mean an end to all of border and security arrangements.
There are several regular flights from Iranian cities to the Kurdistan region.
The news comes hours after Iran’s elite Revolutionary Guards began military exercises along the border with Iraqi Kurdistan.
Such exercises are common in the region, due to the persistent threat posed by Kurdish separatists, who regularly carry out cross-border attacks against Iranian security forces.