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Iran has raised a red flag - symbolising revenge - over the Jam Karan mosque in Qom on Wednesday morning, an indication that it is preparing a response to Israel’s killing of Hamas political bureau chief Ismail Haniyeh,

The flag was previously raised when Iranian Revolutionary Guards Corps (IRGC) commander Qassem Soleimani was killed in a US airstrike in 2020 and after the Kerman cemetery bombings in 2024.

Iranian Supreme Leader Ayatollah Ali Khamenei has also given orders for Iran to directly attack Israel, in response to Haniyeh's killing, The New York Times reported, citing three Iranian officials.

Khamenei issued the order during an emergency meeting of the Supreme National Security Council on Wednesday morning, shortly after Haniyeh was killed in an Israeli attack on the building in Tehran he was staying in.

Two of the three sources The New York Times spoke to were from the IRGC. They requested anonymity because they were not authorised to speak to the media.

The news came as Israeli Channel 12 reported that Israeli Prime Minister Benjamin Netanyahu had been given additional security in anticipation of an Iranian response, following the assassination of Haniyeh in Tehran and the earlier killing of senior Hezbollah commander Fuad Shukr.

The new precautions mean that Netanyahu and other ministers will only be able to take part in public events if there is a nearby safe space.

Israel is widely believed to be behind the strike which killed Haniyeh, who has been heavily involved in negotiations for a ceasefire in the brutal Gaza war which has killed over 39,000 people. It has not yet officially claimed responsibility however.

In a public statement following Haniyeh’s killing, Khamenei said that Israel had opened itself up to “a severe punishment” and indicated that Iran would retaliate directly.

Other Iranian officials, such as recently-elected President Masoud Pezeshkian also indicated that Iran would retaliate, saying that the killing of Haniyeh at a guesthouse for in Tehran was also an attack on Iran’s sovereignty.

Doubts over negotiations

The assassination has seriously compromised Iran’s security reputation, with only a small number of senior security officials allowed to know where Haniyeh was staying.

It has been widely condemned in the Middle East and across the world, with Palestinians declaring a general strike in the West Bank and Qatar, which has played a key role in mediation efforts to end the Gaza war and hosted Haniyeh, reacted furiously.

"Political assassinations and continued targeting of civilians in Gaza while talks continue leads us to ask, how can mediation succeed when one party assassinates the negotiator on the other side?" Qatari Prime Minister��Mohammed Bin Abdul Rahman al-Thani��said.

Three US officials told Axios that the Biden administration is "very concerned" that Haniyeh’s assassination could halt Gaza ceasefire negotiations and spread the conflict.

White House spokesperson John Kirby however told reporters on Wednesday that it is "too soon to know"��how the assassination would impact negotiations.

Last April, Iran launched hundreds of drones and missiles at Israel in retaliation for an Israeli airstrike on the Iranian consulate in Damascus which killed seven senior commanders.

The attack had a limited impact however, with little damage caused and most of the projectiles intercepted by Israel.