United States officials say the Iranian scientist who has claimed he was kidnapped and tortured by American agents had been a CIA informant for years.
The scientist, Shahram Amiri, flew back to Tehran from the US on Thursday.
He disappeared last year while in Saudi Arabia on a pilgrimage, and resurfaced Washington in July asking to go home.
The New York Times reports that the scientist had, while inside Iran, been an informant for US intelligence officers, citing unnamed US officials.
The paper says he gave details of how a university in Tehran became the covert headquarters for the country's nuclear efforts, and was one of the sources for a disputed National Intelligence Estimate on Iran's suspected weapons program, published in 2007.
The US has insisted the scientist had arrived in the United States of his own free will and that there had been nothing stopping him from leaving.