While U.S. Secretary of State Hillary Clinton said Shahram Amiri had been in the United States of "his own free will" and could leave when he wanted, the scientist claimed to have been captured by CIA operatives while on a pilgrimage in June 2009.
There have been a series of contradictory videos posted on the Internet about whether Amiri had defected to the United States or was being held against his will. This week he went to a Pakistani diplomatic mission and asked to be sent back to Iran.
There were also conflicting reports about Amiri's role in Iran's nuclear program. Tehran claimed he was a university researcher but there were signs he had important information about Iranian's nuclear projects. The Washington Post cited unnamed U.S. officials as saying Amiri disclosed "significant information" about Tehran's nuclear program.
U.S. intelligence sources told The New York Times Amiri may have become concerned about the safety of family members in Iran and decided to return to his home country.
Early Wednesday Iranian state-run media said Amiri was out of the United States and en route to Iran.
Many Western countries claim Iran is trying to develop a nuclear weapons capability. Tehran says its nuclear program is for civilian purposes.