"They also are able to both train and support and finance, and so that capability is still significant," he said.
Mullen added that the US military is "very focused on making sure that it doesn't happen again," referring to the potential for another such attack on US soil.
Meanwhile, Al-Qaeda is gaining from the support of Taliban fighters in Afghanistan and Pakistan, making the US fight against extremism in Afghanistan all the more urgent, Mullen said.
"I think it (the situation in Afghanistan) is serious and deteriorating and I've said that over the last couple of years, that the Taliban insurgency has gotten better, more sophisticated."
US support for the war in Afghanistan has appeared tepid at best. A survey by the Washington Post and ABC News in mid-August suggested 51 percent believe the war is not worth fighting, while 47 percent support it.
"Certainly the numbers are of concern," Mullen said, as Washington ramps up efforts to bolster the size and strength of US forces in Afghanistan.
President Barack Obama, who has made the conflict a top priority in his administration and declared the war there a "necessity," has ordered the deployment of 21,000 additional troops which would boost the total to 68,000 by the end of the year.
The White House is also expecting within two weeks an evaluation by the commander of US forces in Afghanistan, General Stanley McChrystal, who may cut the number of troops in support staff roles to free up soldiers for combat against Taliban insurgents.
McChrystal, who oversees American and NATO troops in Afghanistan, is weighing the step as he carries out an assessment of the war effort amid widespread speculation he is preparing to request more US troops.
While the Pentagon has said the official recommendation will not include a request for troops, Washington expects such a request in the coming months.
US Independent Senator Joseph Lieberman, who recently met with McChrystal in Afghanistan, confirmed that a request would be forthcoming.
"We didn't talk about it in detail. But it's very clear that General McChrysal is going to ask for more troops," he said on CNN's State of the Union talk show.
US media has reported that McChrystal is considering three options, including a "high risk" strategy of adding just 15,000 troops to the 68,000 troops that would be on the ground by year's end.
A "medium risk" strategy would add 25,000 troops and a "low risk" option would be to send in 45,000.
Arizona Senator John McCain said his concern was that McChrystal would not produce a recommendation for a discrete number of troops based on needs on the ground.
"I'm not happy with what he's going to do -- it will be 'high risk,' 'medium risk,' 'low risk'," the Republican former presidential candidate told ABC news.
"Whenever you do that, they always pick the medium risk," McCain said.
"I think he ought to do what General (David) Petraeus did (in Iraq), and that's decide exactly on the number he needs and then we debate it," he added.
"We need to know exactly what resources he needs," McCain said.
Republican Senator Richard Lugar, also appearing on CNN's State of the Union, warned that Obama would need offer strong backing for McChrystal's report and requests.
"I think the president really has to face the fact that his own leadership here is critical. He really can't just leave this to the Congress, to General McChrystal, and say, folks, sort of, discuss this after the report comes in."
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