Gen Stanley McChrystal spoke on the eighth anniversary of the September 11, 2001, attacks on the United States by al Qaeda that prompted the 2001 US-led invasion of Afghanistan.
The invasion quickly toppled the Taliban regime that had sheltered al Qaeda leaders who plotted the 9/11 attacks, but has since bogged down amid a deadly insurgency.
"I do not see indications of a large al Qaeda presence in Afghanistan now," McChrystal told reporters at the Dutch Defence Ministry, where he met military officials.
But he warned that Osama bin Laden's network still maintains contact with insurgents and seeks to use areas of Afghanistan they control as bases.
"I do believe that al Qaeda intends to retain those relationships because they believe it is symbiotic ... where the Taliban has success, that provides a sanctuary from which al Qaeda can operate transnationally," he added.
The spectre of al Qaeda terrorists being harboured by insurgents in lawless areas of Afghanistan serves as a reminder to America and its allies of why the increasingly unpopular war started.
Last month, McChrystal sent a "strategic assessment" of the war to US and NATO leaders. He has not revealed its contents publicly, but said at the time that success in Afghanistan "is achievable and demands a revised implementation strategy, commitment and resolve, and increased unity of effort."
Earlier this year, President Barack Obama ordered 21,000 more troops to Afghanistan, which will bring the total number of US forces there to 68,000 by the end of the year.
McChrystal is expected to ask for more troops soon, but would not elaborate on numbers on Friday.
"My position here is a little bit like a mechanic. We've got a situation with a vehicle and I've been asked to look at it and tell the owner what the situation is and what it will cost to make the vehicle run correctly and I will provide that," he said.
"Now I understand that the vehicle owner then has to make a decision on what the car is worth, how much longer he intends to drive it," he added. "Whether he wants it to look good or just run."
McChrystal can expect the US Congress to take a long look at any cost estimate he sends them.
Speaker Nancy Pelosi, the highest-ranking Democrat in Congress, said this week she did not think "there's a great deal of support for sending more troops to Afghanistan in the country or in the Congress."
But while scepticism about the war in Afghanistan grows, McChrystal said allied troops there likely prevented other terror attacks since 9/11.
"We have not been struck again in the United States, and I think the strikes that would have hit across the world — not just in Europe or the United States but I think also in much of the Muslim world — I think have been prevented," he said. "I can't prove that because you can't prove a negative, but I certainly strongly believe that is the case."
The Hague: The top commander of US and international forces in Afghanistan said on Friday he sees no signs of a major al Qaeda presence in the country, but says the terror group still maintains close links to insurgents.
First Published: Friday, September 11, 2009, 20:57