Iran’s supreme leader has called for the “definitive punishment” of those behind the killing of one of the country’s most senior scientists, who was identified by Israel as having headed a secret nuclear weapons programme. Mohsen Fakhrizadeh, the architect of Tehran’s nuclear strategy, was killed on Friday on a highway near the capital in a carefully planned assassination that has led to a serious escalation of tensions in the Middle East. Iran accused its arch-enemy, Israel, of carrying out the attack. Expecting retaliation, Israel put its global embassies on high alert on Saturday, Hebrew-language media reported. In a statement, Ayatollah Ali Khamenei called Fakhrizadeh “the country’s prominent and distinguished nuclear and defensive scientist”. Iran’s immediate priority, he said, was the “definitive punishment of the perpetrators and those who ordered it”. He did not elaborate. Speaking during a meeting of his government’s coronavirus taskforce, the Iranian president, Hassan Rouhani, blamed Israel and reiterated that Fakhrizadeh’s death would not stop the country’s nuclear programme, which it claims is non-military and focused on energy. During the past decade, Iran has accused Israel of killing at least five of its nuclear scientists, although Fakhrizadeh is considered the most senior and high-profile. “We will respond to the assassination of Martyr Fakhrizadeh in a proper time,” Rouhani said, suggesting it could be days or weeks before a retaliation. Iran later told the UN in a letter there were “serious indications of Israeli responsibility” and that it reserved the right to “take all necessary measures to defend its people”. During past spikes in hostility, Iran’s proxy in Lebanon, Hezbollah, has carried out attacks on Israeli targets. An Israeli military spokesperson said it would not “comment on reports in the foreign media,” while the country’s prime minister’s office also remained silent. Donald Trump, who had Iran’s most powerful general killed in a drone strike earlier this year, has not spoken about Friday’s attack. However, in a possible hint of his support, the outgoing US president retweeted an Israeli journalist who described the killing as a “major psychological and professional blow for Iran”. Concerns have mounted in the Middle East that Israel might use the final weeks of the Trump administration to take action. The US president is generally seen in Israel as more permissive of its ambitions, both political and military, than the president-elect, Joe Biden. To Israel’s dismay, Biden has said he is willing to rejoin the Iran nuclear deal abandoned by Trump and lift some economic sanctions if Iran comes back into compliance with the agreement. Israel and regional powerhouse Saudi Arabia want the US to remain outside the deal. Trita Parsi, the executive vice-president of the Washington-based Quincy Institute thinktank, said Israel was a “prime suspect”, and suggested the country carried out the killing to damage any attempt by Biden to rebuild the US’s relationship with Iran. “The main impact of attacks of this kind will not be to set back Iran’s programme but to render diplomacy for Biden more difficult,” he said, adding that Israel’s leader, Benjamin Netanyahu, has long sought to drag Washington into a confrontation. Without suggesting who carried out the killing, Amos Yadlin, a former head of Israeli Defence Force intelligence, said: “With the window of time left for Trump, such a move could lead Iran to a violent response, which would provide a pretext for a US-led attack on Iranian nuclear facilities.” John Brennan, a former head of the CIA under Barack Obama, called the assassination “a criminal act and highly reckless”. “Iranian leaders would be wise to wait for the return of responsible American leadership on the global stage and to resist the urge to respond against perceived culprits,” he tweeted. The spokesperson for Josep Borrell, the EU’s foreign policy chief, described the attack as a “criminal act” and called for “all parties to remain calm and exercise maximum restraint”. Fakhrizadeh was ambushed with explosives and gun fire in the town of Absard, 70km (44 miles) east of Tehran. Efforts to resuscitate him in hospital failed. His bodyguard and family members were also wounded. The scientist had been described by western and Israeli intelligence services for years as the leader of a covert atomic bomb programme halted in 2003. He was a central figure in a presentation by Israel’s Netanyahu, in 2018 accusing Iran of continuing to seek nuclear weapons. “Remember that name, Fakhrizadeh,” Netanyahu said during the presentation. Netanyahu accused Iran at the time of hiding and expanding its nuclear weapons knowhow, saying that Israeli intelligence had obtained a half-tonne cache of nuclear archive materials from the country. Iran has always denied it has any interest in developing nuclear weapons. During the final months of Trump’s presidency, Israel has been making peace with Gulf Arab states that share its hostility towards Iran. This month, Netanyahu travelled to Saudi Arabia and met its crown prince, according to Israeli officials, in the first reported visit by an Israeli leader. Agencies contributed to this report