Mehrdad Bazrpash said on Sunday that Saudi Arabia’s flag airline had forwarded the request to the Civil Aviation Organization of Iran.
He said the three flights would not include Hajj-related flights.
Bazrpash said relevant Iranian organizations would do their best to schedule the flights.
Iran and Saudi Arabia announced an agreement to reestablish relations on March 10 followibg seven years of cut ties.
The two countries are expected to reopen their embassies before Hajj season in June.