Tel Aviv, Israel - Iran launched hundreds of drones and missiles in an unprecedented overnight attack on Israel that marks a major escalation of the long-running covert war between the regional foes.

Iran had repeatedly threatened to retaliate against Israel for a deadly April 1 air strike on its Damascus consular building – a direct attack on Iranian territory – and the US had warned in recent days that the reprisals were imminent.

"Last night Iran fired over 300 ballistic missiles, UAVs, and cruise missiles towards Israel," military spokesman Rear Admiral Daniel Hagari told a televised statement

The Israeli army said it had scrambled dozens of fighter jets to intercept "all aerial threats", and worked with the US and other allies to stop 99% of the launches.

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"The Iranian attack was foiled," Hagari instisted.

US President Joe Biden reiterated Washington's "ironclad" support for Israel after an urgent meeting with his top security officials on the spiraling crisis.

Iran's Revolutionary Guards confirmed a drone and missile attack was launched against Israel in retaliation for the Damascus strike that killed seven Guards, two of them generals.

The Guards said ballistic missiles were fired almost an hour after the slower moving drones.

Hundreds of Iranians gathered in Tehran's Palestine Square, waving Iranian and Palestinian flags in a show of support for the military action against Israel.

Iran's allies in the region joined the attack, with Yemen's Tehran-backed Houthi rebels also launching drones at Israel, according to security agency Ambrey.

Lebanon's Hezbollah movement announced it had fired rockets at Israeli positions in the annexed Golan Heights around the same time, as well as a second barrage hours later.

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Tehran's official IRNA news agency said the attack had dealt "heavy blows" to an air base in the Negev desert, but the Israeli army said there had only been minor damage.

The Iranian mission to the UN warned Washington to keep out of Iran's conflict with Israel.

"It is a conflict between Iran and the rogue Israeli regime, from which the US MUST STAY AWAY!" it said.

It added that it hoped Iran's action to punish the strike on its diplomatic mission would lead to no further escalation and "the matter can be deemed concluded".

Axios reported that Biden had told Netanyahu he would oppose an Israeli counterattack against Iran and that he should "take the win".

British Prime Minister Rishi Sunak condemned Iran's "reckless" action and pledged his government would "continue to stand up for Israel's security."

France echoed the commitment to Israel, with Foreign Minister Stephane Sejourne saying "Iran has reached a new level of destabilization."

Egypt, which regularly acts as a mediator between Israel and the Palestinians, said it was in "direct contact with all sides to the conflict to try to contain the situation."

And regional powerhouse Saudi Arabia urged parties to exercise "restraint and spare the region and its peoples from the dangers of war".

China, meanwhile, characterized the attack as "the latest spillover of the Gaza conflict" and called for the implementation of a recent UN Security Council resolution demanding a ceasefire in the besieged Palestinian territory, saying more than six months of fighting "must end now".

The Security Council is set to meet Sunday to discuss the latest crisis at Israel's request, its current president Malta said.

Biden said he would also convene his fellow leaders of the G7 group of wealthy nations on Sunday to coordinate a "united diplomatic response" to Iran's "brazen" attack.

Earlier on Saturday, Iran's Revolutionary Guards seized an Israeli-linked container vessel in the Gulf earlier on Saturday, putting the whole region on alert.