Shaukat Aziz did say, however, that Pakistan's relationship with the US remained important and that he would depart as planned on Tuesday for an official visit to Washinton.
He made the comments, regarding the supposedly CIA-organised strike apparently aimed at Ayman al-Zawahri, al-Qaida's second-in-command, in a joint press conference with George Bush, the former US president.
Bush Sr is touring Pakistan as the UN secretary-general's special envoy for the relief effort in areas affected by the earthquake in October.
Aziz said: "Pakistan has committed to fighting terrorism but naturally we cannot accept any action within our country which results in what happened over the weekend. The relationship with the US is important, it is growing. But at the same time such actions cannot be condoned."
Friday's attack on the village of Damadola, near the Afghan border, has become an embarrassment for Islamabad. The Pakistan government is a key ally of the United States in its so-called war on terror, but has said it does not allow US forces to track down or attack militants within its territory.
Many Pakistanis oppose the government's support of the US, and there is increasing frustration over a series of suspected US attacks directed at militants along the porous and ill-defined frontier with Afghanistan.
Thousands took to the streets over the weekend, chanting "Death to America" and calling for the resignation of the president, Pervez Musharraf.
Intelligence officials said the missile attack was targeted at al-Zawahri, Osama bin Laden's top lieutenant. The Egyptian-born al-Zawahri had reportedly been invited to dinner in the town, but did not attend.
Many Pakistanis dislike their
country's close ties with the US
Instead, he sent some aides to the dinner, and investigators were trying to determine whether they had been in any of the three houses that were destroyed in the missile strike, which killed at least 17 people, including women and children.
Aziz's ruling Pakistan Muslim League Q party issued a statement on Monday that condemned the attack and demanded an official apology from the US.
Aziz has said that he will take up the matter with George Bush, the US president, when he meets him.