Pakistan closed two NATO supply routes to Afghanistan and shut down Central Intelligence Agency drone operations at the Shamsi air base in western Pakistan, The New York Times reported.
One of the supply routes at Torkham, which runs through the Khyber Pass, is responsible for 40 percent of NATO supplies in the region, the Times said. Reports said some trucks had already been turned back.
The attacks happened Saturday at two northwestern military posts near the border with Afghanistan's Kunar province.
U.S. Marine Gen. John Allen, commander of NATO-led forces, quickly responded with condolences for those killed or wounded in the attacks.
"My most sincere and personal heartfelt condolences go out to the families and loved ones of any members of Pakistan security forces who may have been killed or injured," Allen said in a statement.
"This incident has my highest personal attention and my commitment to thoroughly investigate it to determine the facts."
Brig. Gen. Carsten Jacobson, a NATO spokesman, said the alliance was investigating how the attacks that occurred about 2 a.m. local time.
Jacobson said a combined Afghan and NATO contingent had been in the area when "a tactical situation developed on the ground," but he did not provide details. He said air support was called in and "we're aware it's highly likely this caused casualties."
Yet to be determined, however, is what specifically happened on the ground that triggered the call for air strikes at the two posts a mile and a half into Pakistan.
"Air force was called in into this activity and we have to look into this situation of what actually happened on the ground," Jacobson said.
Both helicopters and jets responded to the request for help, the Times reported.
The attack, which apparently netted no terrorists, further worsened relations between Pakistan and the United States, NATO's lead country in the mission, the BBC said.
Pakistani Prime Minister Yousuf Raza Gilani labeled the attack "outrageous" and called an emergency meeting of the Cabinet.
Gen. Ashfaq Parvez Kayani, Pakistan's army chief of staff, condemned the "blatant and unacceptable act," and demanded "strong and urgent action be taken against those responsible for this aggression," the military said.
U.S.-Pakistani relations have been deteriorating since the American raid that killed al-Qaida leader Osama Bin Laden in May.
"The relationship is on a much more slippery slope now. This is as close as you can get to a rupture," said Maleeha Lodhi, who has served two stints as Pakistan's ambassador to the United States.