Iranian media reported explosions early on Friday but an Iranian official told Reuters those were caused by air defence systems.
State media said three drones over the central city of Isfahan had been shot down.
Israel's leadership and the military were silent early on Friday.
The United States received notification before Israel's attack, a source familiar with the situation told Reuters, which came days after Iran launched an unprecedented strike on Israel with a barrage of drones and missiles, most of which were shot down.
The attack came days after Iran launched an unprecedented drone and missile strike on Israel. (AP PHOTO)
Washington and other global powers had pressed to Israel not to respond, or to ensure any further retaliation was limited to prevent a broader conflagration after the latest surge in violence was sparked by the air strike on the Iranian embassy compound in Damascus on April 1 that was blamed on Israel.
That strike came against the backdrop of Iran's support for the Palestinian Hamas militant group, whose assault into Israel on October 7 triggered Israel's invasion of Gaza.
Iranian state TV said on Friday that shortly after midnight "three drones were observed in the sky over Isfahan".
"The air defence system became active and destroyed these drones in the sky," it said.
Senior army commander Siavosh Mihandoust was quoted by state TV as saying air defence systems had targeted a "suspicious object".
Iranian President Ebrahim Raisi had warned Israel before Friday's strike that Tehran would deliver a "severe response" to any attack on its territory.
Iran told the United Nations Security Council on Thursday that Israel "must be compelled to stop any further military adventurism against our interests" as the UN secretary-general warned that the Middle East was in a "moment of maximum peril".
Shares and bond yields sank in Asia trade while safe-haven currencies, gold and crude oil jumped.
IAEA can confirm that there is no damage to — IAEA - International Atomic Energy Agency ⚛️ (@iaeaorg) #Iran's nuclear sites. DG @rafaelmgrossi continues to call for extreme restraint from everybody and reiterates that nuclear facilities should never be a target in military conflicts. IAEA is monitoring the situation very closely. pic.twitter.com/4F7pAlNjWMApril 19, 2024
Iran's state television said nuclear facilities where Iran has been conducting work - which Tehran says is peaceful but which the West believes is aimed at building a weapon - were unharmed.
The International Atomic Energy Agency confirmed there was no damage to Iran's nuclear sites, and called for extreme restraint from all sides.
The Natanz nuclear site, the centrepiece of Iran's uranium enrichment program, is in Isfahan province.
Iran closed its airports in Tehran, Shiraz and Isfahan after the attack and also cleared flights from the western portion of its airspace for a few hours after the attack, according to FlightRadar24.
The airports and airspace had reopened by 8.15am, Tehran time (2.45pm AEST).
Israel's assault on Gaza began after Palestinian Islamist group Hamas attacked Israel on October 7, killing 1200, according to Israeli tallies.
Israel's military offensive has killed more than 33,000 Palestinians in Gaza, according to the local health ministry.
Iran-backed groups have declared support for Palestinians, launching attacks from Lebanon, Yemen and Iraq.
