Shahram Amiri disappeared a year ago while on a pilgrimage to Saudi Arabia.
A video broadcast by Iranian TV purports to show Mr Amiri saying he was kidnapped and is living in Arizona.
Hours later, another video posted on YouTube appeared to show the scientist saying he was happy in America. The US denied abducting him.
"Since I was abducted and brought to the US I was heavily tortured and pressured by US intelligence" Shahram Amiri http://news.bbc.co.uk/2/hi/world/middle_east/10269255.stmThe contradictory accounts of Mr Amiri's fate have emerged as the UN Security Council is due to vote on a fourth round of sanctions against Iran over its nuclear programme on Wednesday.
Mr Amiri worked as a researcher at a university in Tehran, Iranian media reported.
But other reports said he worked for the country's Atomic Energy Organisation and had in-depth knowledge of the country's nuclear programme.
In the video shown on the Islamic Republic of Iran Broadcasting network, the man says he was forced to say he defected with a laptop full of evidence about Iran's nuclear secrets and that he was being used to put pressure on Iran.
The video showed a man wearing headphones and talking to his webcam.
He says he was in the Saudi city of Medina as part of a Muslim pilgrimage when Saudi intelligence officers drugged and kidnapped him.
"When I became conscious, I found myself in a plane on the way to the US," he said.
"Since I was abducted and brought to the US I was heavily tortured and pressured by US intelligence."
The man says in the film that the recording was made on 5 April in the city of Tucson, Arizona.
Iranian TV reports said the Iranian security services obtained the film "by special methods" but did not elaborate.
"I am Iranian and I have not taken any steps against my homeland" Shahram Amiri. (Second broadcast)On Monday the clip was posted on YouTube.
Responding to the allegation on Tuesday, state department spokesman Philip Crowley told reporters: "Did the United States kidnap [Mr Amiri] from Saudi Arabia? The answer is No."
In the second clip, posted hours later to a YouTube account in the name of Shahramamiri2010, the man says he lives safely in the city and wants to continue his education in the US.
"I am free here and I assure everyone I am safe," he said in Farsi.
"My purpose in today's conversation is to put an end to all the rumours that have been levelled at me over the past year. I am Iranian and I have not taken any steps against my homeland."
In March US news channel ABC ran a report quoting unnamed US officials that said Mr Amiri had defected and was helping the US compile intelligence on Iran's nuclear weapons programme.
They suggested that he had given them valuable information about the Iranian nuclear programme, including the recently revealed centrifuge enrichment plant outside the city of Qom.
The secret plant was revealed in September last year, just days before a meeting in Geneva between Iran and the permanent five members of the UN Security Council.
The US and its allies believe Iran is trying to acquire a nuclear weapon, but Tehran denies the charge.
Jon Leyne, BBC Tehran correspondent
It is a tale of two videos. A murky story, as might be expected when the Iranian and American secret services cross paths.
Neither video is entirely convincing. The Iranian government version is poor quality, with the possibility that it has been manipulated.
In the YouTube video, the man is looking beyond the camera, apparently reading a not very well written script.
The US government has never spoken about the case publicly. But officials told American news organisations in March that Mr Amiri had defected.
Officials said it was an "intelligence coup". They claimed it was the fruit of a wider operation, using contacts through the many Iranians now living in the United States, to obtain access to the Iranian nuclear programme.
There also seems to be an element, on both sides, of psychological warfare, not to mention propaganda, as each side plays up the quantity of inside information they have gleaned from inside each other's countries.