US Ambassador Cameron Munter was told "that such strikes were not only unacceptable but also constituted a flagrant violation of humanitarian norms and law," the ministry said in a statement.
Pakistan's civilian and military leaders have already condemned Thursday's drone strike against a militant hideout in North Waziristan tribal region and demanded an apology and explanation from the US.
Civilians and police were among those killed when US missiles ploughed into a compound in Datta Khel town, 40 kilometres (25 miles) west of Miranshah, the main town in tribal North Waziristan.
Intelligence sources in Peshawar said the dead included 12 Taliban militants.
Frosty diplomatic relations with the US appeared to have thawed Wednesday after a Pakistan court released a CIA contractor, accused of double murder, after $2 million in blood money was paid to the families of the dead.
His release sparked protests from ordinary Pakistanis on Friday, with festering anti-US sentiment among demonstrators further inflamed by Thursday's missile strike.
US drones have frequently targeted Datta Khel, known as a stronghold of the Taliban commander and Al-Qaeda-linked warlord Hafiz Gul Bahadar, and the Peshawar official said the militants hit were members of the Pakistani Taliban.
The ministry said that Munter was met by foreign secretary Salman Bashir who conveyed "a strong protest" over the CIA-operated pilotless drone attack.
"It was evident that the fundamentals of our relations need to be revisited. Pakistan should not be taken for granted nor treated as a client state," the statement said.
"It was for the White House and the State Department to hold back those who have been trying to veer Pakistan-US relationship away from the track."
The ministry said Pakistan would now not attend a meeting in Brussels with officials from the Washington and Kabul on security in Afghanistan, scheduled for March 26.
Ambassador Munter said he understood that Islamabad's protest was not a "pro forma demarche" (a formality) and that he would swiftly convey its message to the highest levels of the US administration, the ministry said.
A security official said the missile strike killed about two dozen civilians, including tribal leaders and elders.
"They were part of a jirga or council of tribal elders, mediating a dispute between two local tribes in Datta Khel district," a security official said.
The jirga had been convened to resolve a feud between two local groups over the ownership of a disputed mine in the region, residents said.
"The drones appeared about 30 minutes after the jirga started and fired four missiles at the gathering of 50-60 people. I was wounded and fell unconscious," Inamullah Khan, who lost a leg, told AFP at a state-run hospital in Miranshah.
Missile attacks doubled in the area last year to more than 100, killing over 670 people in 2010 compared with 45 strikes that killed 420 in 2009, according to an AFP tally.
Most have been concentrated in North Waziristan, the most notorious Afghan Taliban and Al-Qaeda bastion in Pakistan, where the United States wants the Pakistan military to launch a ground offensive as soon as possible.
Pakistan says its troops are too overstretched to launch an assault.