Mostafa Ahmadi-Roshan died after an unidentified motorcyclist stuck a magnetic bomb to his vehicle, according to the Iranian media.
The 32-year-old academic had been working at the Natanz uranium enrichment facility.
Iranian officials blamed the bombing on Israel, which they claim is trying to derail the country¡¯s nuclear programme.
Israel has denied the charge, and along with the US, claims that Iran is attempting to build a nuclear weapon.
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Tehran says that the enrichment programme is for peaceful purposes.
Safarali Baratloo, deputy Tehran governor, is quoted on BBC online saying: ¡°The bomb was a magnetic one and the same as the ones previously used for the assassination of the scientists, and the work of the Zionists [Israelis].¡±
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The blast, the latest in a series of attacks on nuclear scientists in Iran, reportedly took place near Tehran¡¯s Allameh Tabatai university.
Mr Ahmadi-Roshan supervised a department at Natanz uranium enrichment facility in Isfahan province, the semi-official Fars new agency reported.
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