An anti-aircraft system destroyed one drone and two others exploded, the ministry said, adding there were no casualties and only minor damage to the site in the central province of Isfahan.
A fireball lit up the night sky in video footage widely shared on social media and published by Iranian state media, with people outside seen running and emergency service vehicles speeding toward the site.
“An unsuccessful attack was carried out … on one of the workshop complexes of the ministry of defence,” the ministry said, according to state news agency IRNA.
“The attack, which occurred around 11:30 pm (2000 GMT) on Saturday, did not cause any disruption to the operation of the complex,” it said.
Authorities did not elaborate on the activities at the site, but IRNA said the strike had targeted “an ammunition manufacturing plant”.
Parliament member Mohammad-Hassan Assafari told the Mehr news agency that “opponents and enemies” of Iran were aiming to “disrupt the defencive power” of the country with the attack.
The drone strike comes at a tense time in Iran, which has been rocked by protests over the death in custody of Kurdish-Iranian woman Mahsa Amini in September, and as the standoff with major powers over its nuclear programme remains unresolved.
Iran has also faced accusations by Western countries that it has been supplying armed drones to Russia for use in the war in Ukraine, a charge Tehran denies.