Licences will now only be granted to "relevant bodies and not individuals", military officials said.
The unmanned aerial devices have caused several security scares after approaching sensitive areas.
Drones have become increasingly popular in Tehran, but have angered locals who believe they infringe their privacy.
"These quadcopters are equipped with cameras and can fly over sensitive sites, film them and be exploited by the enemy," said deputy commander of the Islamic Revolution Guards Corps (IRGC), Ali Reza Rabi'i.
