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 U.N. sanctions because of their work on suspected nuclear weapons development.
The U.N. 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.