The Hindustan Times said Dr Y.S.R. Prasad took up an assignment in Iran after he retired in July 2000 as head of the Nuclear Corporation of India.
The revelations come as Tehran begins to yield to international demands to prove it is not developing nuclear weapons and to make a complete declaration of all its past nuclear activities.
Iran had promised Tuesday to provide the information following talks in Tehran with the foreign ministers of Britain, France and Germany.
The Hindustan Times, quoting from a classified government document, said Prasad, who spent years working on India's atomic energy programmes, did not seek government permission to go to Iran.
It said that while the scientist did not break any rules, the government was now seeking to make it compulsory for India's nuclear experts to seek government approval for foreign assignments.
It quoted government sources as saying that while New Delhi and Tehran do have a strategic partnership, they do not collaborate in nuclear programmes.
India stunned the world in 1998 by conducting five nuclear tests and declaring itself a nuclear power. Rival neighbour Pakistan conducted its own tests within days.
Meanwhile, a director of an Indian company accused of exporting chemicals to Iraq for its missiles programmes has been denied bail in a New Delhi court, the Press Trust of India news agency reported.
Hans Raj Shiv was arrested on Tuesday at Delhi's international airport when he arrived from a trip abroad.
He and his company NEC Engineers, are charged with aiding Saddam Hussein's attempts to rearm Iraq by supplying prohibited materials.