Petraeus told Bloomberg News: "The Taliban has, in a sense, regenerated [and] reconnected in these communities where they were dispersed to after being defeated at the end of 2001.
"They gradually came back together ... and then, over time, re-established the infrastructure - they built cells and structures to the point where now 33 or 34 provinces have [a] shadow governor," he said.
"That has outstripped the efforts of Isaf forces being built over time, to the point that we really have to get ahead of that."
Anders Fogh Rasmussen, the Nato secretary-general, said earlier in the day that members of the military alliance needed to support the training of Afghan security forces to prevent the country becoming a haven for Taliban and al-Qaeda fighters.
"We are not in Afghanistan to protect and defend a specific government, but to make sure Afghanistan does not once again become a safe haven for terrorists who could easily spread from Afghanistan through Central Asia and further," he said.
"I urge all allies to provide resources for this training mission so that the Afghans can eventually take over responsibility for the security themselves."
Obama on Wednesday held a meeting of national security advisers to discuss options for Afghanistan, but the following day he left for a nine-day tour of Asia without a decision being announced.
Robert Gates, the US defence secretary, said Obama wanted the announcement on troop levels to "signal resolve and at the same time, signal to the Afghans as well as to the American people that this isn't an open-ended commitment".
While en route to Tokyo on Thursday to kick off a nine-day tour of Asia, Obama stopped at the Elmendorf air base in Alaska and told US troops there that his government would not risk US soldiers' lives unless absolutely necessary.
Wednesday's meeting reportedly focused on four possible options for a revised US strategy, and how long each would take to implement.
The US currently has nearly 68,000 troops deployed to fight a resurgent Taliban and al-Qaeda in Afghanistan. As Obama debates a revised strategy in the eight-year war, officials say he is considering four options.
One option is the request put forward by the top US commander in Afghanistan, General Stanley McChrystal, for 40,000 more troops to secure the towns and cities.
Another option, said to be carrying the most favour among officials, is an increase of 30,000. Washington could then try to convince Nato allies to contribute, bringing the number of troops to the 40,000 McChrystal recommended.
Options three and four include significantly lower troop deployments, from 20,000 to 15,000, most of who would serve as trainers for the Afghan security forces.
But Gates said that deliberations were now focusing on how to "combine some of the best features of several of the options to maximum good effect".
"There is a little more work to do. I do think that we're getting toward the end of this process."
The US defence secretary also said he was "appalled" by the amount of media leaks that had accompanied the decision-making process in the White House.
Media reports on Wednesday said that the US ambassador to Afghanistan had expressed strong reservations about an increased troop deployment.
According to the New York Times and Washington Post, Karl Eikenberry, writing in classified cables to top US officials, expressed worries over the Afghan administration and its ability to tackle widespread corruption that has spurred the Taliban's revival.
Eikenberry was also quoted as saying that additional troop deployments would only increase Afghanistan's reliance on US security forces.
The US already has about 68,000 troops in Afghanistan. About 38,000 of those soldiers are fighting under the mandate of the 71,000-strong multinational Isaf force.