One source told Reuters the U.S. was not involved but was notified by Israel before the attack.
Iran's Fars news agency reported three explosions were heard near an army base in the central city of Isfahan. An Iranian official told Reuters there was no missile attack and the explosions were the result of the activation of Iran's air defense systems.
Iranian state TV said that shortly after midnight "three drones were observed in the sky over Isfahan. The air defense system became active and destroyed these drones in the sky."
The broadcaster later said the situation in Isfahan was normal and no ground explosions had occurred.
The Israeli military had no comment on the reports.
Israel had said it would retaliate against Iran's weekend attack, which involved hundreds of drones and missiles, in response to a suspected Israeli strike on its embassy compound in Syria. Most of the Iranian drones and missiles were downed before reaching Israeli territory.
Analysts and observers have raised concerns about the risks of the Israel-Gaza war spreading into the rest of the region.
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 U.N. secretary-general warned that the Middle East was in a "moment of maximum peril."
Asian shares and bond yields sank on Friday while safe-haven currencies, gold and crude oil jumped. Brent crude futures LCOc1 rose 2% to $88.86 a barrel, the dollar gained broadly, gold XAU= rose 1% and S&P 500 futures ESc1 dropped 1%. MKTS/GLOB
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 Natanz nuclear site, the centerpiece of Iran’s uranium enrichment program, is in Isfahan province.
Airports in Tehran, Shiraz and Isfahan were closed until 0700 GMT, subject to extension, and flights have been cleared from the western half of Iran, slight tracking website FlightRadar24 reported.
Some flights destined for Tehran from Turkish Airlines and Emirates were returning to their origin, FlightRadar24 said on X. An Iran Air flight from Rome to Tehran was diverting to Ankara, Turkey, it showed.
FlightRadar24 showed Emirates, flydubai, Turkish Air, Wizz Air Abu Dhabi and Belavia were among the carriers continuing to use the part of Iran's airspace that remained open on Friday morning.
Israel's assault on Gaza began after Palestinian Islamist group Hamas attacked Israel on Oct. 7, killing 1,200, according to Israeli tallies. Israel's military offensive has killed over 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.