The air strike which took place on Friday was apparently aimed at aimed at Osama bin Ladin's deputy and al-Qaida's second-in-command, Ayman al-Zawahiri.
Intelligence officials said US counterparts had told them the order for the strike was based on information that al-Zawahiri, had been invited to a dinner at a village in the Bajaur tribal region near the Afghan border.
Two Muslim clerics known for harbouring al Qaida fighters attended but left hours before the raid and al-Zawahiri did not show up, they said.
US intelligence sources said al-Zawahiri's fate would not be known until remains of the dead were examined.
Although the US government has not publicly acknowledged any responsibility, intelligence officials in Washington with knowledge of the operation said it was aimed at al-Zawahiri and said they believed drone aircraft armed with missiles were used.
Pakistan, a key US ally in the war on terrorism, condemned the attack and summoned the US ambassador to protest at the deaths of civilians, who included women and children.
The incident provoked anti-American protests in several Pakistani towns and cities on Sunday, and supporters of a party allied with Pervez Musharraf, the Pakistan president, were among 10,000 people who rallied in the southern city of Karachi.
Thousands joined anti-US rallies
across Pakistan after the strike
About 200 members of the student wing of Pakistan's main Islamist party, Jamaat-e-Islami, protested in Karachi again on Monday, chanting "Down with America", "Bush is a symbol of
terrorism" and "Musharraf is a traitor".
Condoleezza Rice, the US secretary of state, said Washington could not deal "lightly" with al-Qaida in Pakistan, but promised to address Islamabad's concerns over such strikes.
Speaking on her way to Liberia, Rice gave no details of the air strike, but said the border area had been lawless for some time and US forces were trying to help Pakistani troops who were operating there.
The Muttahida Majlis-e Amal (MMA) opposition Islamist alliance has called for a debate in parliament on the issue this week, which could prove uncomfortable for Musharraf.
"America raised the bogey of al-Zawahiri to provide justification for this attack," Meraj-ul-Huda, an MMA leader, told Monday’s rally in Karachi rally, echoing remarks by Pakistani officials speaking privately.
Pakistani newspaper editorials denounced the attack and warned it would fuel support for Muslim fighters.
"The strike would be unjustified even if it took out the targeted figures," said The News, an English-language daily.
"America raised the bogey of al-Zawahiri to provide justification for this attack"
"Apart from the element of Pakistan's sovereignty, this country is the United States' partner in the 'war on terror'," it said, adding that the attack could "supply an excellent new case for the fanatics".
The Daily Times said there was reason to believe it was a joint operation based on information from the Pakistani side.
The deaths only added to Musharraf's problems, the paper said, pointing to a long-running and bloody struggle against al Qaida-linked fighters in another tribal area and government efforts to suppress the Baluchistan insurgency.