Iran has accused the CIA of kidnapping Shahram Amiri, who worked for Iran's Atomic Energy Organization. The United States did not say how Amiri got there but denied kidnapping him and said he was always free to leave.
Iran is locked in a dispute with the United States and its allies over Tehran's nuclear development program that the West says is designed to produce nuclear weapons and which Iranian officials say aims to generate power.
Amiri on Wednesday gave a dramatic version of a cloak-and-dagger operation to abduct him.
Iran's Foreign Ministry spokesman said Amiri was on his way back to Iran after surfacing at the Iranian interests section of the Pakistan Embassy in Washington D.C. on Monday. Washington cut ties with Tehran after Iran's 1979 Islamic revolution.
"With the ... effective cooperation of Pakistan's Embassy in Washington, a few minutes ago Shahram Amiri left American soil and is heading back to Iran via a third country," Ramin Mehmanparast said on television.
Another Foreign Ministry official said Amiri was expected to arrive in Tehran on Thursday via Qatar.
"Amiri will return home via Qatar. He will be welcomed by officials at Tehran's Imam Khomeini International Airport on Thursday," said Hasan Qashqavi, state TV reported.
Amiri is provisionally expected home at roughly 2300 GMT Wednesday.
Iran said the Foreign Ministry would pursue Amiri's case through legal and diplomatic channels to nail down what part the US government played in the saga.
The State Department said the United States did not kidnap Amiri, but it has not addressed whether another country might have abducted him and turned him over.
A man identifying himself as Amiri has variously said in recent videos that he was kidnapped and tortured; that he was studying in the United States; and that he had fled US agents and wanted human rights groups to help him return to Iran.
Amiri was quoted by Iranian state TV on Tuesday as saying "my kidnapping was a disgraceful act for America."
The mystery surrounding Amiri fueled speculation that he may have had information about Iran's nuclear program sought by US intelligence. In March, ABC News reported that Amiri had defected and was helping the CIA.
Intelligence about the program is at a premium for the United States, which fears that a nuclear-armed Iran would threaten its close ally, Israel, as well as oil supplies from the Gulf and friendly nations in Europe.
Asked why Amiri was going back, a US official suggested that Iranian authorities might have influenced his family.
"He may well be feeling some pressure from back home. The Iranians aren't beyond using family to influence people. That could be one explanation for his contradictory messages," the official, who spoke on condition of anonymity, told Reuters.
He also sought to cast doubt on Amiri's account, saying the fact that he was free to make videos and to leave undercut his claim of coercion.
Amiri said he would reveal more details on his arrival in Iran.
"I have a very long and detailed story ... I have explained some key parts in the footage broadcast in the past."
