Updated 10.50am Sunday

Iran on Sunday urged Israel not to retaliate militarily to an unprecedented attack overnight, which Tehran presented as a justified response to a deadly strike on its consulate building in Damascus.

"The matter can be deemed concluded," Iran's mission to the United Nations said in a post on social media platform X just a few hours after the start of the operation late Saturday.

"However, should the Israeli regime make another mistake, Iran's response will be considerably more severe," the Iranian mission warned.

No Iranian leaders have spoken out yet to justify the attack, which marked the first time Iran has launched a direct military assault on Israeli territory.

On Saturday Iran launched more than 200 drones and missiles on Israel in a major escalation of the long-running covert war between the regional foes.

Iran's proxies and allies also carried out coordinated attacks on Israeli positions as sirens sounded in many places and AFP correspondents heard blasts in the skies above Jerusalem early Sunday caused by missile interceptions.

The Israeli army said the vast majority of Iran's missiles were intercepted.

"Only a few missiles fell in the territory of the state of Israel with slight damage to a military base in the south, with only slight damage to the infrastructure," Rear Admiral Hagari said in a statement. 

Iran's official IRNA news agency had reported earlier that the "most important Israeli air base in the Negev was the successful target of the Kheibar missile."

"Images and data indicate that the base sustained heavy blows," it said. 

Iran had repeatedly threatened to strike Israel in retaliation for a deadly April 1 air strike on its Damascus consular annexe where two senior Iranian generals were killed. IRNA said the air base in the Negev was used by Israel to hit the Iranian consulate in Damascus..

"Iran launched UAVs from its territory towards the territory of the state of Israel," military spokesman Daniel Hagari said in a televised statement.

"We are working in close cooperation with the United States and our partners in the region in order to act against the launches and intercept them," Rear Admiral Hagari said.

Israel also requested Malta, as president of the UN Security Council, to convene an urgent meeting. The meeting has been scheduled for later on Sunday.

People in Jerusalem sought cover, as residents also stockpiled water.

"As you can see it's empty, everybody is running home," said Eliyahu Barakat, a 49-year-old grocery shop owner in Jerusalem's Mamilla neighbourhood.

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

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

The Guards said its 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 to celebrate the unprecedented military action against Israel.

The Israeli army said Iran had launched a "massive swarm of over 200 killer drones, ballistic missiles and cruise missiles".

The army said it had scrambled dozens of fighter jets to intercept "all aerial threats".

Iran's allies in the region joined the attack with Yemen's Huthi rebels also launching drones at Israel, according to security agency Ambrey, and Lebanon's Hezbollah movement announcing rocket fire at Israeli positions in the annexed Golan Heights.

Iran-backed Hezbollah, which has regularly traded cross-border fire with Israel since the start of the ongoing war in Gaza, said in a statement that it had launched "dozens of Katyusha rockets" at three Israeli military positions in the Golan, which Israel seized from Syria in the Six-Day War of 1967.

The 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.

'Keep out'

The Iranian mission to the United Nations 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 U.S. MUST STAY AWAY!" it said.

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

But a Pentagon official said US forces were shooting down drones which had been aimed at Israel.

Early Sunday, the office of Israeli Prime Minister Benjamin Netanyahu said he had spoken with Biden.

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

The defence ministry said it had moved several additional fighter jets to the region which stood ready to "intercept any airborne attack within range".

France echoed the commitment to Israel's security. "In deciding to take this unprecedented action, Iran has reached a new level of destabilisation," Foreign Minister Stephane Sejourne said.

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".

Malta schedules UN Security Council for Sunday

Israel asked Malta, as president of the United Nations Security Council to convey an urgent meeting. The meeting will be held at 8pm GMT on Sunday.

Shortly before the launches, Netanyahu said Israel was prepared for a "direct attack from Iran".

"Our defence systems are deployed, we are prepared for any scenario, both in defence and attack," the Israeli premier said.

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

Israel said it was closing schools nationwide while Jordan, Iraq and Lebanon announced they were temporarily closing their airspace.

Israel said it was closing its own airspace from 2130 GMT.

The Israeli military warned Iran it would suffer the "consequences for choosing to escalate the situation any further".

The April 1 strike in Damascus, which killed 16 people, including two Iranian generals, had been widely blamed on Israel. Iran had repeatedly vowed to hit back, but had not specified how.

Iran's Revolutionary Guards seized a container ship "related" to Israel in the Strait of Hormuz on Saturday, which was heading towards Iranian waters, Iranian state media reported.

The ship's operator, the Italian-Swiss group MSC, said it was working with the relevant authorities to ensure the wellbeing of the 25 crew onboard.

Both Israel and the United States denounced the seizure as piracy, with Israel also demanding the Guards be declared a "terrorist organisation" by the European Union.

Gaza truce stalemate

The Gaza war began with the unprecedented October 7 attack by Palestinian militants Hamas against Israel which resulted in the deaths of 1,170 people, mostly civilians, according to an AFP tally based on Israeli figures.

Israel's retaliatory offensive has killed at least 33,686 people in Gaza, mostly women and children, according to the territory's Hamas-run health ministry. 

Israel's military said Saturday it had struck more than 30 Hamas targets across Gaza.

In the main central city of Deir al-Balah, fire burned in the rubble of a destroyed mosque.

Israel's military "demanded that the whole area be evacuated" before it was "wiped out in minutes", said Abdullah Baraka, a witness.

Hamas said it had submitted its response to a Gaza truce plan presented by US, Qatari and Egyptian mediators at talks in Cairo this week. 

The Palestinian militant group said it was sticking to its previous demands, insisting on "a permanent ceasefire" and the "withdrawal of the occupation army from the entire Gaza Strip".

Attack 'telegraphed'

Experts have suggested that Saturday's slow-moving drone attack was calibrated to represent a show of power but also allow some wiggle room.

"It appears that Iran telegraphed its attack on Israel to demonstrate it can strike using different capabilities, to complicate the (Israeli army's) ability to neutralise the assault but also to provide an off-ramp to pause escalation," said Nishank Motwani, senior analyst at the Australian Strategic Policy Institute in Washington.

"Tehran can escalate if it chooses to across a range of vectors," said Motwani, including via Lebanon's Iran-backed armed group Hezbollah, sea attacks, "or hitting soft Israeli targets globally".

Over the last two weeks, the Iranian authorities had repeatedly vowed to "punish" Israel after the death of seven Guards including two generals of the Quds Force in the attack that levelled the Iranian consulate in Damascus.

Iran has blamed Israel for the attack.

In the days after the strike, Iran's Supreme leader Ayatollah Ali Khamenei said Israel will be "slapped for that action".

Since a revolution in 1979 in Iran which toppled the US-backed Shah, Israel has been the sworn enemy of the Islamic republic.

Iran has often called for the destruction of Israel, with support of the Palestinian cause one of the pillars of the Islamic revolution. 

However, until Saturday Tehran had also refrained from a direct attack on Israel.

Instead, it has backed members of the so-called "Axis of Resistance" against Israel, including Hezbollah and Yemen's Tehran-aligned Huthi rebels, since the outbreak of war in Gaza between Israel and Palestinian militant group Hamas on October 7.

Hours before the strikes on Saturday, Iran seized an Israeli-linked container ship in the Gulf which Washington called "an act of piracy".