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.
"As flying objects, especially those of heli-shots [drones equipped with cameras]... they can pose a threat," the commander said, according to the Tasnim news agency.
In December, a drone was shot down after it entered a no-fly zone near the offices of the country's top officials, including Supreme Leader Ayatollah Ali Khamenei.
The drone, reported to have been owned by state television, was said to have been filming for a documentary.
Another incident last month saw the Khatam al-Anbia air defence system fire anti-aircraft guns at an unidentified drone over the centre of Tehran, but it failed to destroy the device.
Officials said on Monday that permits must now be obtained for all drones, but they will not be issued to individuals.