The Natanz facility, which is located in the desert in the central province of Isfahan, is the centerpiece of Iran's uranium enrichment program and monitored by inspectors of the International Atomic Energy Agency, the U.N. nuclear watchdog.
"The incident caused no casualties or contamination," Iran's Atomic Energy Organization spokesman Behrouz Kamalvandi said, adding that "electricity was affected at the Natanz facility".
The cause was being investigated, Kamalvandi told Iran's semi-official Fars news agency.
A spokesman for the U.N. nuclear watchdog said by email : "We are aware of the media reports. We have no comment at this stage."
In July last year, a fire broke out at the Natanz facility, which the government said was an attempt to sabotage Iran's nuclear program. In 2010, the Stuxnet computer virus, widely believed to have been developed by the United States and Israel, was discovered after it was used to attack Natanz.