The men are accused of running a prison at this Kabul house
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The US State Department says three US citizens arrested in Afghanistan are counter-terrorism mercenaries operating outside Washington's command.
Spokesman Richard Boucher said the US government "does not employ or sponsor" the three, who were arrested by Afghan authorities on Monday.
Afghan officials accuse the men of running a private prison in Kabul.
Correspondents say the US bounty for al-Qaeda fugitives has drawn many foreign vigilantes to Afghanistan.
The US government has promised $25m for anyone who facilitates the arrest of al-Qaeda kingpin Osama Bin Laden.
Mr Boucher confirmed that one of the arrested men was Jonathan K Idema, who has described himself as a counter-terrorism expert and former US commando.
One of those arrested with him was named as Brent Bennet; the third man was not identified.
Mr Boucher said the question of what the men "were being held for and what charges might be proffered" was a matter for the Afghan authorities.
'Rebels'
Four Afghans were also detained along with the three US citizens.
The prisoners are now reportedly in the hands of Afghan intelligence officials.
Afghan Interior Minister Ali Ahmad Jalali said the arrested men's activities had no legal standing.
"They apparently said that their aims were to act against those carrying out terrorist attacks," Mr Jalali told journalists in Kabul.
"But they did not have a legal relationship with anyone and the United States was also chasing them - they are actually rebels," he said.
Bestselling book
US officials say Mr Idema had tried to pass himself off as an American government or military official.
Earlier this week the US embassy warned journalists in Kabul about Mr Idema who says he helped anti-Taleban rebels fight the hardline Islamist regime back in 2001.
"The public should be aware that Idema does not represent the American government and we do not employ him," a US statement said.
Security sources have told the BBC that the US military circulated warning notices about Mr Idema some time ago, describing him as armed and dangerous and accusing him of interfering with military operations in Afghanistan.
Mr Idema has offered his services to the western media as an expert on fighting the Taleban and al-Qaeda and has also featured in a bestselling book, The Hunt for Bin Laden.