The US ambassador to Afghanistan says he does not believe that Osama Bin Laden or Taleban chief Mullah Omar are in the country.
Mr Khalilzad was careful to avoid offending Pakistan
He did not say where the two men are but correspondents say his comments imply that they could be in Pakistan.
A senior Taleban commander said on Wednesday that the two men were alive and well.
Pakistani President Pervez Musharraf says that his forces have "broken the back" of al-Qaeda in his country.
"Mullah Omar is not in Afghanistan. I do not believe that Osama is in Afghanistan," US Ambassador Zalmay Khalilzad said at a news conference in Kabul.
He was speaking at his final press conference before taking up his next post as US ambassador to Baghdad.
"It is not an easy job to find one person, maybe with some (people) helping him... in a vast region.
Mr Khalilzad had particular influence in Afghanistan
"It requires timely intelligence," he said.
The ambassador said that "a lot of progress" has been made in fighting al-Qaeda and that it was not clear how much control Osama Bin Laden still has over it.
"Significant numbers of the leaders of al-Qaeda have been captured. Their network has been disrupted... the financial network has also been disrupted," he said.
"But this is a long-term struggle, and symbolically (it is) very important that he (Bin Laden) is brought to justice, and sooner or later I believe firmly that he will be caught."
The US has offered $25m for Osama bin Laden's capture
US officials have long argued that the Bin Laden is hiding somewhere on the border between Afghanistan and Pakistan.
Mr Khalilzad has been a controversial figure. Last year Pakistan denounced comments he made about Islamabad not doing enough to fight al-Qaeda as "worrisome, foolish and highly irresponsible".
Correspondents say that Mr Khalilzad was careful to try to avoid offending Pakistan in his latest comments about Osama Bin Laden by using more diplomatic language.
'Alive and well'
Speaking at a meeting at the end of his three-day visit to Australia, President Musharraf said that his forces had chased al-Qaeda out of the cities into the mountains and then "occupied their sanctuaries".
"Terrorism is to be confronted with force. We are doing that, and we have succeeded," Gen Musharraf told a meeting of businessmen in Sydney.
His comments came a day after a Taleban commander claimed that Osama Bin Laden and Afghanistan's former Taleban leader Mullah Omar are alive and well.
"I am in contact with Mullah Omar and take directions from him," Mullah Akhtar Usmani told Pakistan's privately-run Geo television.
"Taleban are all over Afghanistan," he said, "they may be more in some provinces and less in the other, but their support is growing."
There is no way of independently verifying Mullah Usmani's claims.
Correspondents say that Mr Khalilzad has been the US ambassador in Kabul since November 2003, and has played a hugely influential role in Afghanistan's transition process.
The Afghan-American will soon replace John Negroponte as US ambassador to Iraq.