"It was inactive and there was no radioactive material in it and there were no personnel", the organisation's spokesman, Behrouz Kamalvandi told state TV.
However, this was largely disputed by defense analysts as satellite photographs of the Parchin complex emerged showing large amounts of damage at the site. "Thank God, the site is continuing its work as before".
The nuclear plant, 250 kilometers (155 miles) south of Tehran, consists of underground nuclear enrichment facilities and is one of the sites monitored by the International Atomic Energy Agency (IAEA).
Th site includes underground facilities buried under some 7.6 meters (25 feet) of concrete, which offers protection from airstrikes.
Iran has faced a series of explosions throughout the country over the last couple of weeks, but no foul play has been reported so far at any of the sites of the incidents, although some media outlets alleged that Israel was involved in the events.
Natanz governor Ramezan-Ali Ferdowsi told the Tasnim news agency that a fire had broken out at the warehouse.
After the Trump administration pulled out of a nuclear agreement with Iran and other countries in May 2018 and reimposed sanctions on the Iranian economy, Tehran announced it was developing advanced centrifuges able to enrich uranium to weapons-grade levels more quickly - though worldwide inspectors say it has stopped short of producing any such fuel.
Iranian nuclear officials did not respond to a request for comment from the AP on the analysts' findings.
Kamalvandi initially said the fire at the Natanz facility in central Iran caused no damage to "current activities of this complex". Uranium hexafluoride gas is fed into them to separate out the most fissile isotope, U-235.
The Cheetahs claimed in a video that they are "soldiers from the heart of regime's security organizations" who want to stop Iran from getting a nuclear weapon.
"It would delay the advancement of the centrifuge technology quite a bit at Natanz".
Iranian officials have sought to downplay the fire, which erupted early on Thursday, calling it only an "incident" that affected an "industrial shed".
The underground Natanz Fuel Enrichment Plant is one of several Iranian facilities monitored by inspectors of the International Atomic Energy Agency, the United Nations nuclear watchdog.
A massive explosion that rocked the Mahdaj Ahwaz gas production plant near the Az-Zarqan region in Ahwaz province, western Iran on Saturday, came two days after another explosion rocked the nuclear facility in Natanz.
Since the facility itself had not been damaged, said Kamalvandi, there was no concern of possible contamination.
Ashkenazi spoke at a conference marking a decade since Israel joined the Organization for Economic Cooperation and Development (OECD), saying Israel's policy towards Iran has been consistent for years, no matter which government is in power in Jerusalem, the Maariv newspaper reported.