A member of the Iranian Revolutionary Guards Corps confirmed to the Times that an explosive was used in the incident as well. Both officials spoke on condition of anonymity.
Israel has worked to disrupt Iran's nuclear program in the past, including the Stuxnet cyberattack discovered in 2010, which targeted Iran's nuclear centrifuges and was blamed on Israel and the US.
The IRGC member told the Times that the possibility that a cyberattack was behind the incident at Natanz has been ruled out.
Former top Mossad official Haim Tomer told 103FM on Monday that he was not aware of Israel being responsible for the explosion at Natanz, although the "substantial damage" caused in the incident showed that "there's an operational capability here."
Responding to a question about whether the recent extension of Mossad chief Yossi Cohen's term had anything to do with the incidents in Iran, Tomer stated that he leaned towards saying that it was not connected. "Anyone that knows Yossi and the Mossad a little, estimated in recent months that his term would be extended," said Tomer. In response to questions concerning the incident, Foreign Minister Gabi Ashkenazi stated at the online conference of Maariv and The Jerusalem Post that "we take actions that are better left unsaid."
Meanwhile, Defense Minister Benny Gantz told Army Radio that "not every incident that transpires in Iran necessarily has something to do with us... All those systems are complex; they have very high safety constraints and I'm not sure [the Iranians] always know how to maintain them."
An explosion and fire were reported at the Natanz facility on Thursday, part of several reported at Iranian infrastructure sites in the past few weeks.
Iranian reports originally referred the explosion as an "incident" without providing further details. Iran's top security body said on Friday that the cause of an incident and fire at Natanz had been determined and would be announced later.
Some Iranian officials have said it may have been caused by cyber sabotage, with one warning that Tehran would retaliate against any country carrying out such attacks.
An Iranian official has confirmed that the incident impacted Iran's nuclear program, but promised to repair the damage.
"The incident could slow down the development and production of advanced centrifuges in the medium term... Iran will replace the damaged building with a bigger one that has more advanced equipment," Iranian Atomic Energy Organization spokesman Behrouz Kamalvandi said, according to the IRNA state news agency.
Reuters, Lahav Harkov and Anna Ahronheim contributed to this report.