Mohsen Fakhrizadeh was killed in an attack in Absard, a small city east of Tehran, reports say, while Foreign Minister Javad Zarif claims "serious indications" of Israel's role in assassination.
Prominent Iranian nuclear scientist Mohsen Fakhrizadeh has been "assassinated" in an attack outside the capital Tehran.
Fakhirzadeh's death on Friday was confirmed by the semi-official Fars news agency.
State TV said Fakhrizadeh was attacked by "armed terrorist elements."
Iran's president accused Israel of the killing the scientist long suspected by the West of masterminding a secret nuclear bomb programme, state TV reported on Saturday.
"Once again, the evil hands of global arrogance were stained with the blood of the mercenary usurper Zionist regime," a term for Israel, President Hassan Rouhani said in a statement, according to state TV.
"The assassination of martyr (Mohsen) Fakhrizadeh shows our enemies' despair and the depth of their hatred... His martyrdom will not slow down our achievements."
Iran's Supreme Leader AyatollahAli Khamenei promised to retaliate for the assassination and said his nuclear work would continue.
Earlier, Iran's Foreign Affairs Minister Javad Zarif tweeted that there were "serious indications of Israeli role" in Fakhrizadeh's assassination.
"This cowardice – with serious indications of Israeli role – shows desperate warmongering of perpetrators," Zarif tweeted.
"Iran calls on int'l community – and especially EU – to end their shameful double standards and condemn this act of state terror."
In a letter to UN Secretary-General Antonio Guterres and the UN Security Council, Iran said there are "serious indications of Israeli responsibility" in the assassination and it reserves the right to defend itself.
"Warning against any adventuristic measures by the United States and Israel against my country, particularly during the remaining period of the current administration of the United States in office, the Islamic Republic of Iran reserves its rights to take all necessary measures to defend its people and secure its interests," Iran's UN envoy, Majid Takht Ravanchi, wrote in the letter, which was seen by Reuters.
Israel declined to immediately comment on the killing.
Scientist targeted in explosion, machine gunfire
Fakhrizadeh died at a local hospital after doctors and paramedics couldn't revive him.
The top nuclear scientist was also a brigadier general in the Iran Revolutionary Guard Corps.
Witnesses told Fars news agency they heard the sound of an explosion and then machine gunfire in Absard, a small city east of Tehran.
The attack targeted a car that Fakhrizadeh was in, the agency, believed to be close to the country's Revolutionary Guards, said.
State television on its website later published a photograph of security forces blocking off the road.
Terrorists murdered an eminent Iranian scientist today. This cowardice—with serious indications of Israeli role—shows desperate warmongering of perpetrators— Javad Zarif (@JZarif) November 27, 2020
Iran calls on int'l community—and especially EU—to end their shameful double standards & condemn this act of state terror.
All eyes on Israel
No group immediately claimed responsibility for the attack.
Iranian media all noted the interest that Israeli PM Benjamin Netanyahu had previously shown in Fakhrizadeh.
Hossein Salami, chief commander of the paramilitary Guards, appeared to acknowledge the attack on Fakhrizadeh.
"Assassinating nuclear scientists is the most violent confrontation to prevent us from reaching modern science," Salami tweeted.
Hossein Dehghan, an adviser to Iran's supreme leader and a presidential candidate in Iran's 2021 election, issued a warning on Twitter.
"In the last days of their gambling ally's political life, the Zionists seek to intensify and increase pressure on Iran to wage a full-blown war," Dehghan wrote, appearing to refer to US President Donald Trump.
"We will descend like lightning on the killers of this oppressed martyr and we will make them regret their actions!"
Whenever Iran arrests western spies, western officials, media, "experts" & pundits immediately claim they are all innocent "hostages"— Seyed Mohammad Marandi (@s_m_marandi) November 27, 2020
On the other hand, when such spies are able to accumulate enough information to carry out attacks, murder & assassinations, western elites gloat https://t.co/P5O7acld4s
Mastermind behind Amad plan?
Fakhrizadeh is thought by the West and Israel to have headed what the UN nuclear watchdog and US intelligence services believe was a coordinated nuclear weapons programme in Iran. The so-called Amad plan was shelved in 2003.
He has the rare distinction of being the only Iranian scientist named in the International Atomic Energy Agency's 2015 "final assessment" of open questions about Iran's nuclear programme and whether it was aimed at developing a nuclear bomb.
The IAEA's report said that he oversaw activities "in support of a possible military dimension to [Iran's] nuclear programme" within Amad.
Israel has also described the Amad plan as Iran's secret nuclear weapons programme, and says it seized a large chunk of an Iranian nuclear "archive" detailing its work.
"Remember that name, Fakhrizadeh," Israeli Prime Minister Benjamin Netanyahu said in a 2018 speech revealing details from the archive, naming Fakhrizadeh as Amad's chief.
Fakhrizadeh continued working at an organisation within Iran's Defence Ministry on "special projects" even after Amad was shut down, Netanyahu said.
Tehran long has maintained its nuclear programme is peaceful.
The International Atomic Energy Agency says that "Amad" programme ended in the early 2000s. Its inspectors now monitor Iranian nuclear sites.