The US administration has hit back at critics who accuse it of compromising anti-terror efforts by leaking the name of a suspect arrested in Pakistan.
Khan's arrest was kept under wraps - but not for long.
Computer expert Mohammad Naeem Noor Khan was detained in Lahore on 12 July.
He is said to have subsequently helped Pakistani police in secret operations against al-Qaeda - until his name surfaced in the US press last week.
National Security Adviser Condoleezza Rice strongly denied that US officials were responsible for the leak.
"We did not, of course, publicly disclose his name," Ms Rice told CNN television on Sunday.
She said Mr Khan's identity had been given "on background".
Ms Rice did not say when or by whom the name was revealed.
Frances Fragos Townsend, a security adviser to President George W Bush, defended the administration's handling of information provided by Mr Khan about possible al-Qaeda attacks in the US.
"We obviously didn't want to go out with everything that we knew and indicate to the terrorists exactly what we knew," she told Fox News on Sunday.
She said a recent series of arrests in Pakistan and the UK had disrupted al-Qaeda plans to attack the US.
Mr Khan's name first surfaced last Monday, when the New York Times said he had provided most of the information leading to security alerts in New York and other US cities on 1 August.
US officials then confirmed the name to other US news organisations.
THE 'PAKISTAN CONNECTION'
12 July: Khan detained in Lahore
25 July: Ahmed Khalfan Ghailani, wanted for the 1998 US embassy bombings in Africa, captured in central Pakistan
1 Aug: New York authorities warn residents and businesses of a possible new al-Qaeda attacks
3 Aug: 12 terror suspects arrested in raids across England
In recent days intelligence sources both in Pakistan and the UK have criticised the identification of the 25-year-old computer experts.
A Pakistani intelligence official told Reuters news agency that Mr Khan had been actively helping to catch al-Qaeda militants.
Another official in Islamabad quoted by the Associated Press said Mr Khan had agreed to send e-mails to al-Qaeda members as part of a sting operation - which was aborted as a result of his naming.
In Britain, police officers told Reuters they had been forced to arrest 12 terror suspects sooner than they had wanted last week.
The UK sweep occurred a day after Mr Khan was identified.