The ministry said three drones were involved but there were no casualties.
One drone was destroyed by air defence systems and two were caught by "defence traps", causing minor damage to a building, the ministry added.
The extent of damage to the site has not been confirmed by the BBC, and there has been no immediate claim of responsibility.
Iran's foreign minister, Hossein Amir-Abdollahian, said the "cowardly" incident was an attempt to destabilise the country.
