Iranian Supreme Leader Ali Khamenei has ordered a direct attack on Israel following the assassination of Hamas terror chief Ismail Haniyeh in Tehran, the New York Times reported on Wednesday.

Jerusalem has not taken responsibility for the missile strike that killed the Palestinian terror group’s “political” leader and his bodyguard early on Wednesday morning.

Hours after the attack, the Islamic Republic held an emergency meeting of its Supreme National Security Council at the supreme leader’s residence, with the participation of Quds Force commander Esmail Ghaani. Khamenei gave the order at the meeting, according to three Iranian officials – including two members of the IRGC – briefed on the order.

Iran and Hamas accused Israel over the assassination of Haniyeh, who was in Tehran for the inauguration of President Masoud Pezeshkian.

Iranian officials are in “utter shock” over the assassination, sources told NYT journalist Farnaz Fassihi, “because it also delivers a huge blow to Iran’s security reputation at a time it wants to project power in the region.”

Pentagon and US officials were also surprised by Haniyeh’s elimination, and especially that it had taken place in Tehran, the Times reported. While the location of the strike forces the Iranian regime to respond, according to the report, a senior US military official said that despite the security embarrassment Iran may not want to start an all-out war with Israel.

According to the Times report, Iranian military commanders are considering an attack similar to that executed in mid-April, when over 300 drones and missiles were launched at Israel in the first-ever direct attack by Iran on the Jewish state.

The drones and missiles would aim for “military targets in the vicinity of Tel Aviv and Haifa, but would make a point of avoiding strikes on civilian targets,” the Iranian officials said.

One option being considered is a coordinated attack on Israel by Iran and its regional terror proxies, including the Houthis in Yemen and militias in Iraq and Syria.

Iran’s Lebanese terror proxy Hezbollah is also a wild card, with a separate response expected for Tuesday night’s targeted killing by Israel of senior Hezbollah official Fuad Shukr in the heart of Beirut, which was acknowledged by the Israeli military.

The Israel Security Agency has instructed Israeli Prime Minister Benjamin Netanyahu and government ministers to take extra security precautions at public events, Channel 12 reported on Wednesday.

The security instructions come against the backdrop of preparations for an Iranian response to the Haniyeh assassination.

“As part of the instructions given to Netanyahu and the ministers, any participation by them in a mass event requires a protected, close and immediate space. At the same time, the head of the ISA Ronen Bar issued a direct order, according to which every tour conducted by the prime minister and ministers requires his personal approval,” according to the report.

Israeli embassies abroad were also instructed to raise their alert levels and for ambassadors and diplomatic representatives to keep a low profile amid fears of an Iranian attack against Israeli interests abroad.

The security establishment estimates that the Iranian response will occur in the coming days.

Funeral processions for Haniyeh began in Tehran on Thursday morning amid chants of “death to Israel” and signs calling for Israel’s destruction. Many Hezbollah and Palestinian flags were being waved by the crowd, along with posters of Haniyeh.

Hamas in a statement said that after the Tehran funeral, Haniyeh’s body will be taken to Doha, Qatar for burial on Friday.

Based in Doha, Haniyeh was one of the most senior members of Hamas, along with the terror group’s leader in Gaza Yahya Sinwar. The Arab Gulf state, a major financial backer and political ally of Hamas, condemned the assassination.

Khamenei said on Wednesday that Tehran views it as a duty to avenge the killing of Haniyeh.

“The criminal and terrorist Zionist regime martyred our beloved guest inside our house and made us mournful, but it paved the way for a harsh punishment to be imposed on it,” he said in a statement quoted by the state-run IRNA news agency.

Pezeshkian and Iranian Foreign Ministry spokesman Nasser Kanaani also signalled that Tehran would retaliate for the assassination on their soil.

In addition to the attack order, Khamenei also directed IRGC military commanders to prepare defensive plans against an Israeli or US counter-attack.

Speaking during an official visit to the Philippines on Wednesday, US Defence Secretary Lloyd Austin said that the American military would defend Israel if it is attacked.

The Americans led a multinational coalition in April that along with Israel fended off nearly all of the Iranian drones and missiles fired at the Jewish state.

“We certainly will help defend Israel. You saw us do that in April. You can expect to see us do that again,” Austin said, while reiterating Washington’s “unwavering commitment” to Israel’s security.

“We don’t want to see any of that happen. We’re going to work hard to make sure that we’re doing things to help take the temperature down and address issues through diplomatic gatherings,” he added, saying that a wider war in the Middle East is “not inevitable”.

“I think there’s always room and opportunities for diplomacy. What we have seen along the border, northern border, with Israel over time – that’s been a concern of ours. Again, We are going to give everything we can to make sure that we keep things from turning into a broader conflict throughout the region.”

Austin spoke to Israeli Defence Minister Yoav Gallant on Wednesday about the escalating tensions with Hezbollah in Lebanon, stressing American support for Israel’s security.

“They discussed the threats to Israel posed by a range of Iranian-backed terrorist groups, including Lebanese [Hezbollah],” according to the Pentagon’s readout of the call.

“Secretary Austin reaffirmed his unwavering commitment to Israel’s security and right to self-defence. They also discussed ongoing efforts to achieve a diplomatic solution that enables citizens on both sides of the Israel-Lebanon border to safely return to their homes.”

Israel’s Defence Ministry said that Gallant stressed that while the Jewish state does not seek war, the IDF remains “prepared to defend its citizens and to respond to any attack by Hezbollah”.

“Minister Gallant expressed his deep appreciation to Secretary Austin for his personal commitment to Israel’s security, including his public support of Israel’s right to self-defence. He thanked the secretary for his leadership and personal role in maintaining the powerful ties between Israel and the United States,” according to the readout from Jerusalem.

Gallant was also said to have told Austin that the relationship between Jerusalem and Washington is “central to Israel’s standing in the region and to deterring Iran and its proxies.”

Israel remains committed to achieving a hostage deal with the Hamas terror group, especially during these times,” he said.