General John Abizaid, the commander of the US Central Command, said "it is clear" that insurgents are using Pakistan to infiltrate Afghanistan.
"I think that Pakistan has done an awful lot in going after al-Qaeda, and it's important that they don't let the Taliban groups be organised in the Pakistani side of the border."
However, Abizaid said he "absolutely does not believe" accusations of collusion between Pakistan's government and the resurgent Taliban or other extremists.
Afghanistan has repeatedly criticised Pakistan for not doing enough to prevent Taliban insurgents and other fighters crossing the poorly marked border.
Pakistan, a former Taliban supporter but now a US ally, says it does all it can to tackle insurgents and has deployed 80,000 soldiers along the frontier.
Meanwhile, Canadian troops in the south mistakenly killed a policeman and wounded four other officers and two civilians, Nato said on Saturday.
The armed plainclothes police were shot after they did not heed troops' orders to stop as they approached a Canadian checkpoint in a speeding, unmarked vehicle in Kandahar province's Zhari district.
Two other civilians were injured later when the Canadian soldiers fired at their speeding scooter near the same checkpoint. No Canadian troops were reported injured.
Separately, a multinational force air strike killed a local Taliban commander and 15 other insurgents in the central Khod Valley on Friday, the US military said, without identifying the alleged leader.
Afghanistan is experiencing its worst violence since the Taliban was ousted in late 2001 for hosting al-Qaeda leader Osama bin Laden. More than 1,600 people, mostly fighters, have died in the past four months, according to an Associated Press tally of violent incidents reported by US, Nato and Afghan officials.