Frances Townsend, the homeland security adviser to the White House, said there was concern al-Qaeda would "exploit conflict in Iraq and leverage capabilities of al-Qaeda in Iraq, its most visible and capable affiliate".
Her comments echoed an argument that George Bush, the US president, used recently to try to convince Americans that US troops need to remain in Iraq, lest it become a springboard for al-Qaeda attacks.
"Al-Qaeda would have been a heck of a lot stronger today had we not stayed on the offensive," Bush had said.
On Tuesday the White House brushed off critics who allege the administration had released the report, put together from intelligence from 16 US agencies, to influence congressional debate on US troop withdrawals from Iraq.
When asked why Osama bin Laden, the al-Qaeda leader, continued to roam free, Townsend grew irritated.
"It presumes that he sits in a single place with an address ... and a phone number ... and it would be easy to get him. I wish it were that easy ... but it's not," she said.
In September, six years will have passed since Bush said he would get bin Laden "dead or alive" but the report admitted with freedom to operate in havens in Pakistan, al-Qaeda was only getting stronger.
Edward Kennedy, a senator and staunch Bush critic, said: "This has obviously made the war on terrorism harder, not easier, to win.
"Nevertheless the administration turns a deaf ear to all the voices calling for change and continues to plead for more and more time to pursue its failed strategy in Iraq."
The report admitted that al-Qaeda "has been able to restore key capabilities it would need to launch an attack on US soil - a safe haven in Pakistan's tribal areas, operational lieutenants and senior leaders".
It also said al-Qaeda's association with its Iraqi affiliate helped the group to energise the broader Sunni Muslim "extremist" community, to raise resources and to recruit and indoctrinate operatives.
And while it contended that worldwide counter-terrorism efforts since 2001 had constrained al-Qaeda's ability to attack the US again and convinced groups that US soil was now a tougher target, Paul Cruikshank, an analyst from New York University, argued that the so-called "war on terror" was not going well.
"Al-Qaeda is stronger, has more resources, [and is] determined to attack the West," he said.