Iran believes Israel and an exiled opposition group used a remote-control weapon to shoot dead top nuclear scientist Mohsen Fakhrizadeh on Friday.
Security chief Ali Shamkhani said the attackers had "used electronic equipment" when Fakhrizadeh's car was fired on east of the capital Tehran.
He was speaking at the funeral of the scientist Israel accused of secretly helping to develop nuclear weapons.
Israel has not publicly commented on the allegations of its involvement.
In the early 2000s, Fakhrizadeh played a crucial role in Iran's nuclear programme but the government insists its nuclear activities are entirely peaceful.
It has been subjected to crippling Western sanctions aimed at preventing it from developing nuclear weapons.
How did the scientist die?
Iranian versions of what happened have changed significantly but it appears that Fakhrizadeh was mortally wounded when his car was sprayed with bullets in the town of Absard, to the east of Tehran.
During the attack a bomb in a Nissan pickup truck is also reported to have exploded.
Pictures on social media show a road strewn with wreckage and blood, and a bullet-riddled vehicle.
First the defence ministry reported a gunfight between Fakhrizadeh's bodyguards and several gunmen.
One Iranian report quoted witnesses as saying "three to four individuals, who are said to have been terrorists, were killed".
Then Iranian media said the scientist had in fact been killed by a "remote-controlled machine gun" or weapons "controlled by satellite".
And on Monday, Rear Admiral Shamkhani, who heads the Supreme National Security Council, confirmed it had been a remote attack, using "special methods".
"It was a very complex mission using electronic equipment," he said at the funeral. "There was no-one present at the scene."
He said Iranian intelligence and security services had been aware of a plot to assassinate Fakhrizadeh, and had even predicted where the attack might take place.
On who was to blame, he singled out exiled Iranian opposition group the Mujahideen-e Khalq and Israel.
Israel's Intelligence Minister, Eli Cohen, said on Monday in an interview with a radio station that he did not know who was behind the killing.
However, an unnamed senior Israeli official involved in tracking Iranian nuclear activities was quoted by the New York Times as saying that "Iran's aspirations for nuclear weapons, promoted by Mr Fakhrizadeh, posed such a menace that the world should thank Israel".
Machine guns and other remotely controlled ground weapons are now widely used across the Middle East, according to a report by Forbes.
They are employed both by professional armies, such as those mounted on combat vehicles, but also by militants who are known to have put them in vehicles or stationary posts.
Iran's conflicting versions of how its top nuclear scientist was ambushed and killed appear to contradict each other.
The initial account spoke of a dozen armed assailants opening fire on the scientist's convoy and exchanging shots with his bodyguards. The later version, involving both a remote-controlled vehicle and even more bizarrely, a remote-controlled gun, sounds less plausible, although not impossible.
The only way an assassination squad could make sure they had finished the job would be to have eyes on the target. If the earlier version were true then Iran's powerful security and intelligence establishment would face the embarrassing challenge of having to hunt down a large team of assassins just a short drive from the capital.
One thing is clear though: this has been a massive failure of counter-intelligence for Iran's security chiefs and some hard questions are now being asked.
How is Iran responding?
Fakhrizadeh's funeral was held at the defence ministry in Tehran after which his remains were transferred to a cemetery in the north of the capital.
State television showed the flag-draped coffin being carried by troops, and senior officials - including Intelligence Minister Mahmoud Alavi, Revolutionary Guards commander Gen Hossein Salami and nuclear chief Ali Akbar Salehi - paying their respects.
In his own speech at the funeral, Defence Minister General Amir Hatami reiterated Iran's determination to avenge Fakhrizadeh's killing.
"The enemies know, and I as a soldier tell them, that no crime, no terror and no stupid act will go unanswered by the Iranian people," he said.
As head of Iran's Organization of Defensive Innovation and Research, known by its Persian acronym SPND, Fakhrizadeh had carried out "considerable work" in the area of "nuclear defence", the general said.
The government would double the SPND's budget in order to continue the path of the "martyr doctor" with "more speed and more power", he added.
What are regional media saying?
Iranian media are focusing on projecting two main messages - the threat of revenge for the scientist's killing, and a warning that Iran should not "fall into the trap" of what they say are Israel's attempts to escalate tensions over the Iranian nuclear programme.
Israeli media are highlighting the timing of the attack, with analysts interpreting this as a signal to US President-elect Joe Biden that Israel "won't go quietly" if he seeks to rejoin the 2015 Iran nuclear deal. There is also much speculation about possible Iranian retaliation.
Saudi media are reporting the assassination prominently and with interest, given the kingdom's opposition to its regional rival's nuclear programme. A cartoon in the Al-Sharq al-Awsat newspaper appears to mock the Iranian Revolutionary Guards' capabilities. Al Arabiya TV's website meanwhile asks: "Will Fakhrizadeh's assassination affect Biden's approach to Iran?"
Why was Fakhrizadeh a target?
Israeli and Western security sources say Fakhrizadeh was instrumental in Iran's nuclear programme.
The physics professor is said to have led "Project Amad", a covert programme that Iran allegedly established in 1989 to carry out research on a potential nuclear bomb.
The project was shut down in 2003, according to the International Atomic Energy Agency, though Israeli Prime Minister Netanyahu said in 2018 that documents obtained by his country showed Fakhrizadeh led a programme that was secretly continuing Project Amad's work.
In a presentation, Mr Netanyahu urged people to "remember that name".
Iran has previously accused Israel of assassinating four other Iranian nuclear scientists between 2010 and 2012.
Analysts have speculated that the latest assassination was not meant to cripple the Iranian nuclear programme but rather to put an end to the prospect of the US rejoining the 2015 Iran nuclear deal when President-elect Joe Biden takes office next year.
President Donald Trump abandoned the deal in 2018, saying it was "defective at its core", and reinstated US sanctions in an attempt to force Iran's leaders to negotiate a replacement.
Iran has refused to do so and retaliated by breaching a number of key commitments, such as increasing its stockpile of enriched uranium. Enriched uranium can be used to make fuel for nuclear reactors but also potentially nuclear bombs.