About 20 people including civilians are reported to have been killed in the attack on a village in South Waziristan a day earlier.
Both the US-led forces operating in Afghanistan and the separate Nato-led International Security Assistance Force (Isaf) have said they have no knowledge of the incident.
Mowaz Khan, an official in the South Waziristan tribal district, said on Wednesday that helicopters had dropped troops into the border village of Jalal Khel and troops had shot civilians as they left their homes.
Ambassador summoned
The Pentagon has made no official statement, but the Reuters news agency quoted an unnamed Pentagon official as saying the raid had been carried out by special operations forces.
Shah Mehmood Qureshi, Pakistan's foreign minister, summoned Anne Patterson, the US ambassador, and "a very strong protest was conveyed to her", Mohammad Sadiq, a foreign ministry spokesman, said,
Qureshi told the Pakistani parliament: "Only innocent children and women were targeted.
"It is a regrettable, shameful and astonishing incident. We strongly condemn the unprovoked attack by Isaf and coalition forces.
"Coalition forces will have to review their policy. Incidents like this will only fuel hatred among the tribal people."
Parliament later passed a unanimous motion condemning the raid.
The foreign minister's comments threatened to strain Pakistan's relationship with the US, but analysts have speculated that the attack may have received tacit approval from the Pakistani government.
Cross-border raid
Stephen Cohen, a senior fellow in foreign policy studies at the US-based Brookings Institution, told Al Jazeera it was likely the attack had been discussed with general Ashfaq Parvez Kayani, the Pakistani army chief.
He said: "I think this is driven as much by American domestic politics as much as anything else.
"George Bush [the US president] wants to leave office with the record of having captured Osama bin Laden [the al-Qaeda leader] ... I think this raid was an attempt to either capture him or some of the senior al-Qaeda leadership.
"The Americans probably said 'we are going to have to go in and get some of these guys and we don't want to run into Pakistani soldiers on the way in or out' and my guess is that Kayani probably said 'okay do it - were not going to approve it but we're not going to stop it'."
Cohen said the attack appeared to have been carried out by special forces.
"It was a limited attack with a few people. It wasn't a massive military attack.
"The numbers of dead are going to be disputed, but I suspect it was far more precise and targeted than some of the press reports would have it," he said.
"The Pakistanis are unable to ... keep their country clear of these people. They are unable to exercise sovereignty of their own territory so America has decided to exercise sovereignty in their stead."
'Safe haven'
Mahdoum Baba, the editor of Pakistan's Daily Mail newspaper, told Al Jazeera the attacks had provoked angry responses across the country.
"People here are taking [the US attack] like a declaration of war," he said.
"The Americans are very good at creating problems for themselves. This is a highly controversial move taken by the US troops and they are lucky ... Pakistani troops did not retaliate. I believe this action was sort of a rehearsal to attack Pakistan's strategic assets."
Taliban and al-Qaeda fighters are said to have found a safe haven in South Waziristan, where they set up operations when the US invasion toppled the Taliban from power in Afghanistan in October 2001.
US forces say the fighters use bases in Pakistan to launch cross-border attacks on international troops in Afghanistan. Taliban and al-Qaeda fighters have also mounted suicide attacks in Pakistan.
Also on Thursday, a missile attack by what is believed to have been a US drone killed four people in Pakistan's North Waziristan tribal region, and separately Pakistani forces said they killed nearly 40 Pro-Taliban fighters in the country's northwest.
Fighters also kidnapped 26 Pakistani police recruits on their way to college, according to police.