Iranian authorities have repeatedly said that Amiri was seized by the CIA as he visited Saudi Arabia last year – allegations US officials have denied – and Iranian state television broadcast the text of what it said was an interview with Amiri conducted on Tuesday.
'Gun to my side'
Amiri was quoted in the interview as saying that he was abducted at gunpoint by US agents, while attending the Hajj pilgrimage in Saudi Arabia.
"When I opened the door to get in and sit down, the person at the back put a gun to my side and said 'please be quite, don't make any noise'"
Iranian nuclear scientist
"There were three people in the van - a driver, another person in a formal suit and beard, and a third person in the back.
"When I opened the door to get in and sit down, the person at the back put a gun to my side and said 'please be quite, don't make any noise'," he was quoted as saying.
PJ Crowley, a spokesman for the US state department, said on Tuesday that Amiri had been living in the US for "some time".
"I'm not going to specify for how long, but he has chosen to return," Crowley said.
"In fact he was scheduled to travel to Iran yesterday and wasn't able to make all the necessary arrangements to reach Iran through transit countries," he added.
Iran's semi-official Fars news agency said Amiri was handed over to the embassy by US agents, calling it a defeat for US intelligence services.
"He's free to go, he was free to come. Those decisions are his to make"
US secretary of state
"Because of Iran's media and intelligence activities, the American government had to back down and hand over Amiri to the embassy on Monday night," Fars said.
Amiri was quoted in the interview as saying: "They intended to send me back home without much noise in order to cover up the kidnapping through denying the whole case, but they couldn't do that in the end."
When Clinton was asked about the case, she chose instead to focus on the fate of American citizens detained in Iran.
"Iran holds three young Americans against their will and we reiterate our request that they be released and returned to their families on a humanitarian basis," she said.
Sarah Shourd, 31, her boyfriend Shane Bauer, 27, and Josh Fattal, 27, were arrested last July along the Iran-Iraq border and accused of espionage.
Their families say they were simply hiking in Iraq's largely peaceful mountainous northern Kurdish region and that if they crossed the border, it was accidental.
Amiri's fate has been the subject of confusion for weeks. On June 29, Iranian state television aired a video of a man claiming to be Amiri.
|A number of videos purportedly showing Amiri
have appeared on the internet [AFP file]
The man said he had managed to escape from US intelligence agents in the state of Virginia.
"I could be rearrested at any time by US agents ... I am not free and I am not allowed to contact my family. If something happens and I do not return home alive, the US government will be responsible," he said.
"I ask Iranian officials and organisations that defend human rights to raise pressure on the US government for my release and return to my country," the man said, adding he had not "betrayed" Iran.
US officials dismissed the allegations in the Iranian broadcast.
Before that video, two others said to show Amiri appeared on the internet. In the first, broadcast on Iranian TV, a man said he was abducted and was being held in the United States.
He said he was forced to take part in a media interview "to claim that I was an important figure in Iran's nuclear programme and that I had sought asylum in America of my own free will".
In a second video, a man also purporting to be Amiri said he was actually studying in the US.
Iran says it has numerous citizens in secret detention in the US, including a former deputy defence minister who disappeared in 2007.
Earlier this month, Iranian authorities said they had evidence that Amiri had been abducted and had handed it over to the Swiss embassy, which represents US interests in Tehran.