Equipment at the two facilities was moved in anticipation of the strikes, Behrouz Kamalvandi said.
A shed at the Isfahan facility caught fire, Kamalvandi stated, without clarifying the extent of damage to the Fordow site.
There is no risk of contamination, he added.
The Fordow Fuel Enrichment Plant is buried deep in the mountains near Qom in northern Iran and houses advanced centrifuges used to enrich uranium up to high grades of purity.
On Friday, Kamalvandi played down the extent of damage inflicted on Iran’s primary nuclear enrichment plant in Natanz, noting the facility “did not encounter serious damage.”
The head of the United Nations nuclear watchdog however said during a UN Security Council meeting on Friday that the above-ground area of the facility was destroyed.
