The chairman of the US Joint Chiefs of Staff has called for a new strategy in Afghanistan to deny militants bases across the border in Pakistan.
Speaking on the eve of the anniversary of the 9/11 attacks, Admiral Mike Mullen called for a military strategy that covered both sides of the border.
The US must work closely with Pakistan to "eliminate [the enemy's] safe havens", he told Congress.
But Pakistan insists it will not allow foreign forces onto its territory.
"There is no question of any agreement or understanding with the coalition forces whereby they are allowed to conduct operations on our side of the border," Pakistan's Chief of Army Staff, Gen Ashfaq Parvez Kayani, said.
However, the New York Times newspaper reported on Wednesday that President George Bush had approved orders in July to allow US Special Operations forces to carry out ground assaults inside Pakistan without Pakistani approval.
"The situation in the tribal areas is not tolerable," an unnamed senior US official told the newspaper. "We have to be more assertive. Orders have been given."
A surge of US attacks in Pakistan's border region over the past week has prompted outrage from the government and army.
Now stating it as a strategy will only add to the pressure on Pakistan's new President, Asif Ali Zardari, as he grapples with the militants, the BBC's James Coomarasamy reports from Washington.
Adm Mullen was speaking a day after President Bush announced that about 4,500 extra US troops would be sent to Afghanistan by February 2009, boosting the 33,000 currently in the country.
Adm Mullen told the House Armed Services Committee he was not convinced the US was winning in Afghanistan and that a new strategy was needed that addressed the issue of militants in Pakistan.
"In my view, these two nations are inextricably linked in a common insurgency that crosses the border between them," he said.
"We can hunt down and kill extremists as they cross over the border from Pakistan... but until we work more closely with the Pakistani government to eliminate the safe havens from which they operate, the enemy will only keep coming."
Adm Mullen conceded the challenge was great, pointing to Afghanistan's drugs and economic problems, and the "significant political uncertainty" in Pakistan.
The White House said on Wednesday that the failure to capture al-Qaeda leader Osama Bin Laden showed the limitations of US military and intelligence operations.
On the eve of the seventh anniversary of 9/11, White House spokeswoman Dana Perino said President Bush would have liked to see the al-Qaeda leader brought to justice, but that the US authorities did not have "super-powers".
In another development, Canada confirmed its troops would leave Afghanistan by 2011.