An Iranian nuclear scientist who surfaced in Washington more than a year after Tehran claimed he had been abducted by US spies is on his way home, Iran's foreign ministry said today.

"A few moments ago, Shahram Amiri left US soil ... for Iran following efforts taken by the Islamic Republic of Iran and the effective cooperation of the Pakistani embassy in Washington," ministry spokesman Ramin Mehmanparast was quoted as saying by ISNA news agency.

He said Amiri was first headed to a "third country" from where he would continue to Iran, adding that the head of the Iran Interests Section in Washington, Mostafa Rahmani, saw him off.

Repeating accusation that Amiri was kidnapped, Mehmanparast said Iran would continue to pursue his case "legally and diplomatically."

Amiri, who disappeared from Saudi Arabia in May 2009, surfaced in Washington's Iran Interests Section office yesterday.

Iranian officials have maintained that he was kidnapped by the Central Intelligence Agency, a claim which has been vehemently denied by Washington.

US Secretary of State Hillary Clinton told reporters there was nothing stopping Amiri returning to Iran.

"He's free to go. He was free to come. These decisions are his alone to make," she said.