Hundreds of government loyalists surrounded Masoud Ali-Mohammadi's body as it was carried from his home in northern Tehran.
State-controlled television showed them waving Iranian flags and chanting anti-American and antiIsraeli slogans.
Opposition websites reported scuffles between security forces and members of the so-called Green Movement, who also turned up to mourn but were held back. They believe that the regime killed Dr Ali-Mohammadi, on Tuesday because he had switched his allegiance to Mir Hossein Mousavi, the opposition leader.
Unconfirmed reports claimed that security forces kept Dr Ali-Mohammadi's family away from the body. The regime has spent the past three days vigorously promoting the story that Dr Ali-Mohammadi, 50, was killed by foreign enemies with the help of Iranian "mercenaries".
On Wednesday Ali Larijani, the parliamentary speaker, blamed America and Israel for the attack. "We had clear information that the intelligence apparatus of the Zionist regime and the CIA wanted to implement terrorist acts," he said.
However, the regime's narrative is undermined by the lack of any evidence that Dr Ali-Mohammadi was contributing to Iran's nuclear programme, as well as by his declared support for the opposition. Dr Ali-Mohammadi, who taught at Tehran University, specialised in particle physics and was not known to Western officials or agencies which monitor Iran's nuclear programme.
He was one of 420 academics who signed a statement of support for Mr Mousavi during the presidential election campaign last June.
Two former presidents, the reformist Mohammed Khatami and Hashemi Rafsanjani, have issued statements calling Tuesday's bombing an act of terrorism - but by not blaming Israel or America they gave the clear impression that they were blaming the regime.