Pakistani Prime Minister Shaukat Aziz says his country cannot accept a repetition of a US air strike on a village that killed at least 18 people.
The attack has resulted in more pressure on Gen Musharraf
His government also insist it did not share intelligence with the US before Friday's attack, which local officials say also killed four foreign militants.
US reports said the attack targeted al-Qaeda number two Ayman al-Zawahiri.
The US insists relations with Pakistan remain good, and says it will continue to target militants.
"The US clearly values innocent human life, and that is why we're fighting the war on terror," the AFP news agency reported State Department spokesman Sean McCormack as saying.
Mr McCormack added that despite the attack, the US maintained an "atmosphere of co-operation" with the Pakistani government.
The US says it believes al-Zawahiri and Osama Bin Laden are living in the Afghan-Pakistan border region.
"We cannot accept any action within our country which results in what happened over the weekend," Prime Minister Aziz told journalists in the capital, Islamabad.
"So the relationship with the US is important, it is growing, but at the same time such actions cannot be condoned."
A government spokesman said Mr Aziz would raise the issue with President Bush when he meets him in Washington next week.
Initial reports said the missiles had hit a suspected al-Qaeda hideout in Bajaur agency, and that Ayman al-Zawahiri was there. But the reports proved to be incorrect.
The BBC's Zaffar Abbas in Islamabad says the US action has led to fresh domestic pressure on Pakistan's President, Pervez Musharraf, who has been widely criticised for forging a close relationship with Washington.
Pakistan's Information Minister Sheikh Rashid Ahmed said on Tuesday there was no doubt that US forces had carried out the attack.
He also said Western media reports that the bombing was carried out with assistance from Pakistani intelligence agencies were totally baseless.
Officials in Bajaur said on Tuesday that "18 innocent local people" died when three houses were bombed in the village of Damadola village.
Nothing has been heard from Bin Laden in more than a year
But they also said in a statement that at least four to five "foreigners" were killed in the attack but their bodies were removed from the scene.
They say 10 to 12 "foreign miscreants" had been in the village prior to the attack. The statement did not name them or mention al-Zawahiri.
US counter-terrorism ambassador Henry Crumpton has told the BBC that the al-Qaeda leader and his number two are believed to be in the Pakistan-Afghanistan border region.
"We have no intelligence or evidence that indicates that he [Bin Laden] is dead or incapacitated, so our working assumption is that he is still alive."
In Washington, the White House again refused to go into details of the attack.
"I don't ever get into discussing any specific operational activities, or even alleged operational activities," White House spokesman Scott McClellan said.