Iranian officials and state media described professor Massoud Ali-Mohammadi as a nuclear scientist, and Iran's cabinet said agents of the United States were behind his murder.
A State Department official in Washington said charges of U.S. involvement were absurd.
Western sources said Ali-Mohammadi, a physics professor, worked closely with Mohsen Fakhrizadeh-Mahabadi and Fereydoun Abbassi-Davani, both subject to UN sanctions because of their work on suspected nuclear weapons development.
The UN nuclear agency is investigating Iran's nuclear programme, which Tehran says is for generating electricity and not for building nuclear bombs as the West suspects.
Ali Shirzadian, a spokesman for Iran's Atomic Energy Organisation, said Ali-Mohammadi, 50, had not played a role in the activities of the organisation, which is at the centre of the disputed nuclear programme.
Shahram Amiri, a university researcher working for the atomic body, disappeared during a pilgrimage to Mecca in June, three months before Iran disclosed the existence of its second uranium enrichment site near the city of Qom. In December, Tehran accused Saudi Arabia of handing Amiri over to the United States.
"America's spying and intelligence agents from one side abduct some Iranian citizens ... and on the other side their treacherous agents kill an Iranian citizen inside the country," an Iranian cabinet statement said, reported by the semi-official Fars news agency.
A list of Ali-Mohammadi's publications on Tehran University's website suggested his specialism was theoretical particle physics, not nuclear energy, a Western physics professor said.
The bombing -- a rare attack in the Iranian capital -- occurred at a time of heightened tension in the Islamic Republic seven months after a disputed presidential election plunged the oil producer into turmoil.
It also coincided with a sensitive juncture in Iran's row with the West over its nuclear ambitions, with global powers expected to meet in New York on Saturday to discuss possible new sanctions on Tehran over its refusal to halt its atomic work.
Earlier, Iran's Foreign Ministry blamed Israel and the United States.
"Signs of the triangle of wickedness by the Zionist regime (Israel), America and their hired agents, are visible in the terrorist act," it said.
"Such terrorist acts and the apparent elimination of the country's nuclear scientists will definitely not obstruct scientific and technological processes," it said.
White House spokesman Bill Burton said the accusations were absurd. A senior Israeli official said Ali-Mohammadi was not known to have been a significant figurein any military nuclear programme.
English-language Press TV said Ali-Mohammadi was killed in a northern part of the capital by a booby-trapped motorcycle as he was leaving his home. It showed footage of blood stains, broken glass and other debris at the scene, with what appeared to be the dead man in a body bag taken away on a stretcher.
Fars said President Mahmoud Ahmadinejad had ordered the intelligence and security services to use all their capabilities to find those behind the killing.
State broadcaster IRIB described al-Mohammadi as a "committed and revolutionary" professor, suggesting he backed Ahmadinejad's government. Fars quoted one of his students as saying he had worked with the elite Revolutionary Guards until 2003.
But an opposition website, Jaras, said he was an opposition supporter whose name was among hundreds of academics who issued a statement in favour of moderate candidate Mirhossein Mousavi during the campaign for last June's election.
Even if he had worked on Iran's nuclear programme, analysts doubted his death could set back Tehran's aspirations.
"I have no reason to think that this is part of an Israeli or American strategy to deprive Iran of the brains of the enrichment process," said Mark Fitzpatrick, chief proliferation analyst at London's International Institute for Strategic Studies. "There are by now too many scientists and engineers with the requisite expertise".
Stratfor, a global intelligence firm, said Ali-Mohammadi was unlikely to have been a key figure in nuclear activities since his publishing record pointed to purely academic research.
"The relatively high visibility and volume of work in academia suggests that Ali-Mohammadi's role, if any, in the nuclear programme was not very significant," Stratfor said in an analysis. "Critical scientists involved in nuclear weapons programs usually are sequestered carefully and provided more security than Ali-Mohammadi was given."
Fars quoted a foreign-based group, the Iran Monarchy Association, as claiming responsibility for Tuesday's bombing. It did not say how it obtained the statement.
Iran has been convulsed by its most serious domestic unrest since the Islamic Revolution in 1979 as protests by opposition supporters against the election result have turned violent. Authorities deny opposition allegations that voting was rigged.
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