The foreign ministry said that an unspecified number of civilians were also killed in the air raid by an unmanned aircraft.
The foreign ministry said that it had informed US officials of its "great concern".
"With the advent of the new US administration, it is Pakistan's sincere hope that the United States will review its policy and adopt a more holistic and integrated approach toward dealing with the issue of terrorism and extremism," a ministry statement said.
"We maintain that these attacks are counterproductive and should be discontinued,'' it said.
US attacks within Pakistan increased in number in 2008, with more than 30 occurring since August.
Pakistan has previously criticised their effectiveness and consequent deaths of civilians in such attacks. They also say that the air raids heighten anti-US feeling locally and undermine the government's own attempts at halting opposition groups.
The Pakistani parliament has adopted a unanimous resolution stating that US and Nato attacks would be considered an affront to the country's sovereignty.
Obama has not commented on the missile policy but had made the war in Afghanistan and the linked battles against opposition fighters in Pakistan a foreign policy priority.
Richard Holbrooke has been appointed special-envoy for Pakistan and Afghanistan in the Obama administration.
The US does not directly admit to firing missiles in the border region, which Pakistan has little control over.