"IAEA can confirm that there is no damage to Iran's nuclear sites," the Vienna-based agency said on X, adding that it was closely monitoring the situation.
The agency called for "extreme restraint from everybody" and added that "nuclear facilities should never be a target in military conflicts".
Iran's Fars news agency reported "three explosions" were heard near Qahjavarestan, near Isfahan airport and the 8th Shekari army airbase.
Nuclear facilities in Isfahan were reported to be "completely secure", Iran's Tasnim news agency said.
Israel had previously warned it would hit back after Iran fired hundreds of missiles and drones at Israel almost a week ago, in retaliation for a deadly strike -- which Tehran blamed on its foe -- that levelled Iran's consular annex at its embassy in Syria.
IAEA chief Rafael Grossi had said Monday that Iran had closed its nuclear installations for security reasons.
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