"One of (the drones) was hit by the ... air defence and the other two were caught in defence traps and blew up. Fortunately, this unsuccessful attack did not cause any loss of life and caused minor damage to the workshop's roof," the defence ministry said on Sunday in a statement carried by the state news agency IRNA.
Iranian news agencies earlier reported the loud blast and carried a video showing a flash of light at the plant, said to be an ammunitions factory, and footage of emergency vehicles and fire trucks outside the plant.
In July, Iran said it had arrested a sabotage team made up of Kurdish militants working for Israel who planned to blow up a "sensitive" defence industry centre in Isfahan.
The announcement came amid heightening tensions with arch-enemy Israel over Tehran's nuclear program.
Israel says Iran is seeking to develop nuclear weapons. Tehran denies this.
"(The attack) has not affected our installations and mission ... and such blind measures will not have an impact on the continuation of the country's progress," the defence ministry said.
There have been a number of explosions and fires around Iranian military, nuclear and industrial facilities in the past few years.
In 2021, Iran accused Israel of sabotaging its key Natanz nuclear site and vowed revenge for an attack that appeared to be the latest episode in a long-running covert war.
The blasts at sensitive Iranian sites have at times caused concern amid tensions over Iran's nuclear program with Israel and the United States.
Israel has long threatened military action against Iran if indirect talks between Washington and Tehran fail to salvage a 2015 nuclear pact.
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