Ministry spokesman Ramin Mehmanparast said Shahram Amiri was first headed to a "third country" from where he would then continue to Tehran.
An official at the Iranian interests section of the Pakistani Embassy in Washington had told RFE/RL's Radio Mashaal on July 13 that his office was preparing travel documents for Amiri. The official, Ali Sherazi, had said Amiri would be on his way home to Iran on the first available flight.
Pakistan had already confirmed that a man claiming to be the missing scientist sought refuge in that section of its embassy, which is housed in a separate building.
Sherazi told Radio Mashaal that Amiri was in good health, although he said he could provide no further details.
Tehran has long claimed that Amiri was kidnapped by U.S. intelligence agents, and anonymous sources have been quoted as saying he gave CIA debriefers valuable information, presumably on Iran's nuclear efforts.
Until July 13, U.S. officials had maintained an official silence about the case except to deny that it had kidnapped Amiri from Saudi Arabia or any other country.
'Free To Go'
News agencies quoted Iranian Foreign Minister Manuchehr Mottaki as saying on July 13 that Amiri had requested an immediate return to Iran, and that he should be allowed to leave the United States.
But Secretary of State Hillary Clinton reiterated a statement made earlier that day by State Department spokesman Phillip Crowley, who said there was nothing preventing Amiri from leaving.
"Mr. Amiri has been in the United States of his own free will, and he is free to go," Clinton told a news conference in Washington. "In fact, he was scheduled to travel to Iran yesterday but was unable to make all of the necessary arrangements to reach Iran through transit countries."
Clinton then turned the tables, appealing to Iranian authorities in the case of three Americans who crossed the border illegally and that Tehran has accused of spying. The United States has denied the spying charge.
"In contrast, Iran continues to hold three young Americans against their will," Clinton said of Shane Bauer, Sarah Shourd, and Josh Fattal. "And we reiterate our request that they be released and allowed to return to their families on a humanitarian basis."
Sherazi, from the Iran interests section, said Amiri's photos and statement would soon be posted on the Iranian Foreign Ministry's website.
Iran has had no embassy in the United States since diplomatic relations were severed after the 1979 Islamic Revolution, but manages some affairs there through the Iranian Interim Interest office within the Pakistani Embassy.
A Pakistani Foreign Ministry spokesman, Nadeem Patyala, told RFE/RL's Radio Mashaal that a man calling himself Amiri had arrived at the Iran interests section of the embassy on the evening of July 12 asking for shelter.
He gave no other details but said the matter was being dealt with by Iranian officials in the interests section, which is based in a separate building around 3 kilometers from the main embassy compound, rather than by Pakistan's diplomats.
"He was there yesterday evening, dropped [off] by somebody at 6:30 in the evening," Patyala said. He said the Iran interests section "is not the Pakistani Embassy. Pakistan has nothing to do with it other than we are working as a bridge for communication purposes with the U.S. side."
Patyala's remarks confirmed reports, first aired on Iranian state television and radio, which said Amiri was seeking immediate repatriation to Iran. The reports represent the latest twist in the mystery over Amiri, whom Tehran claims was abducted last year in Saudi Arabia during a religious pilgrimage.
A recent series of contradictory videos has further complicated the riddle.
In footage released on Iranian television in June, a man identifying himself as Amiri said he had been taken to the United States and tortured after being abducted in Saudi Arabia.
"My name is Shahram Amiri. Today is April 5, 2010. I am in Tucson, in the United States, caught up in an operation between the U.S. and Saudi Arabia," the man in the video says.
"I was kidnapped in Medina, Saudi Arabia, and injected with something. I was unconscious for several days, during which time I was transferred to the U.S. In eight months in the United States, I was subjected to the worst kinds of torture and pressure."
However, a second video posted on the video-sharing website YouTube days later showed a similar-looking man claiming to be Amiri declaring that he was free in the United States.
"I am in America and intend to continue my education in this country," he said. "I am free here and assure everyone I am safe."
In a third video, shown on Iranian television on June 29, a man describing himself as Amiri said he was in hiding and escaping from U.S. "agents" in Virginia and urged human rights groups to help him return to Iran.
"I could be re-arrested at any time by U.S. agents.... I am not free and I'm not allowed to contact my family," he said, adding that he had not "betrayed" Iran. "If something happens and I do not return home alive, the U.S. government will be responsible."
Then, in a fourth video that appeared quickly on the heels of the third one, a similar-looking man identifying himself as Amiri said he would be returning home.
U.S. officials dismissed the allegations in the broadcast.
Amiri identified himself in one video as "an expert and researcher at Tehran's Malek Ashtar University of Technology," which "The Washington Post" says U.S. intelligence agencies believe has close ties with Iran's Islamic Revolutionary Guards Corps (IRGC).
In March, ABC News reported that Amiri had defected to the United States and was helping the CIA. Anonymous intelligence officials have been quoted in U.S. media as saying Amiri provided valuable information during extensive CIA debriefings.
Some have speculated that Amiri might have been lured out of Iran as part of a U.S. effort referred to casually as "brain drain," which seeks to draw Iran's technically trained elite out of the country.
"The New York Times" reports that Amiri "at some point...was placed in the [U.S.] national resettlement program, a sort of witness-protection program for defectors run by the CIA, and starting in the spring his nervousness about the fate of his wife and child grew markedly."
The same newspaper says Amiri is believed to have worked at a military research facility called Lavizan, which was leveled six years ago amid questions by international atomic inspectors about possible highly enriched uranium at the site.
Reuel Marc Gerecht, a former Middle Eastern specialist in the CIA's clandestine service, told RFE/RL that he believes the CIA would not have kidnapped Amiri. "There is no doubt the agency didn't kidnap him. The agency simply wouldn't do that; it's not productive for them to do that, it's not in their daily work," he said.
Gerecht, now a senior fellow at the Foundation for Defense of Democracies, said Amiri's decision to return to Iran might have been prompted by threats by the regime to his relatives.
Or, he said, Amiri may have simply had a change of heart. Whatever the reason, Gerecht said his return to Iran could be "rough."
"If the gentleman did come out -- and it appears that he did with [CIA] help and assistance -- if he did come out and now he's trying to go home, I think his odds of survival are probably quite poor unless the regime wants to use him for a short period of time as a propaganda tool before applying rough justice," Gerecht said.
At the State Department, spokesman Crowley had few details to offer reporters.
"He has been in the United States for some time. The United States government has maintained contact with him," Crowley said.
"I can't tell you specifically when he made this decision to return to Iran, but...he is here of his free will and this is his decision to depart, and we are helping to facilitate his departure," Crowley added.
Asked by a reporter why the government had maintained contact with Amiri while he was here, Crowley replied, "I can't answer that question."
with contributions by RFE/RL's Radio Mashaal correspondent Majeed Babar and additional agency reports