The latest U.S.-Pakistan crisis is threatening to undo months of efforts to mend an increasingly frayed relationship, and could also undermine the Obama administration’s strategy for gradually ending the war in Afghanistan.

Administration officials did not respond Monday to Pakistani demands for an apology for the cross-border U.S. airstrike that killed at least 24 Pakistani soldiers early Saturday. Instead, they expressed condolences for the loss of life while saying that the facts about what happened were under investigation.

On Tuesday, Pakistan’s cabinet decided to boycott a key international conference on Afghanistan’s future, set to take place on Dec. 5 in Bonn, Germany. Pakistan’s participation, and its cooperation in the wind-down to the war in Afghanistan, is important in large part because of the leverage it is believed to have over the Taliban.

Both sides said they believed they were attacking insurgents along the border Saturday when the strike was launched. A senior Pakistani defense official acknowledged that Pakistani troops fired first, sending a flare, followed by mortar and machine-gun fire, toward what he said was “suspicious activity” in the brush-covered area below their high-altitude outpost barely 500 yards from the border.

According to Afghan security officials, their commandos were engaged with U.S. Special Operations troops in a nighttime raid against suspected Taliban insurgents when they came under cross-border fire and called in an airstrike.

Despite extensive coordination mechanisms set up to prevent such encounters, the U.S. military failed to respond to Pakistani alerts that its troops were being bombed, said the Pakistani defense official, who spoke on the condition of anonymity because he was not authorized to discuss the issue on the record.

“We told them, hold your horses, these are ours,” the official said. While repeated urgent appeals went up the coalition chain of command, he said, the airstrike continued for an hour and a half against two Pakistani border positions and a contingent of troops.

Administration and U.S. defense officials raised the possibility of a different set of circumstances but declined to elaborate.

“Where we are is that we’ve regretted the loss of life and said there should be an investigation,” said a U.S. official who agreed to speak about the tense situation only on the condition of anonymity. “We've just got to put one foot in front of the other here.”

The Pentagon placed the U.S. Central Command in charge of the inquiry, and Centcom’s commander, Gen. James N. Mattis, announced Monday that a Special Operations officer would head it. Air Force Brig. Gen. Stephen Clark was directed to include representatives of NATO and the Pakistani and Afghan governments on the investigation team and to report his conclusions by Dec. 23.

Pakistani anger rising

The investigation, however, risked being overtaken by events in Pakistan, where the government and military commanders are under strong pressure from the increasingly anti-American Pakistani public and the ranks of the army to end counterterrorism cooperation with the United States.

“You cannot win any war without the support of the masses,” Pakistani Prime Minister Yousuf Raza Gilani told CNN. “We need the people with us.” Gilani said that “business as usual” with the United States could not continue.

Pakistan has blocked NATO supplies transiting to Afghanistan at two border crossings and threatened to withdraw from an international conference on Afghanistan next week in Germany. A small contingent of U.S. personnel at Shamsi air base in southern Pakistan was told to leave within 15 days.

Relations were already fractured after a series of clashes this year, including the January shooting death of two Pakistanis in Lahore by a CIA contractor, the U.S. raid that killed Osama bin Laden in Pakistan in May and public U.S. charges that Pakistan’s intelligence service has aided Afghan insurgent networks within its borders.

“You crawl back” from those incidents, the U.S. official said, “and then there is this. There is no question, this is the worst.”

The administration views Pakistani cooperation as crucial to its hopes of bringing Afghan insurgents to the negotiating table within the next year and developing a regional trade zone that could ultimately allow Afghanistan’s economy to prosper without massive foreign aid.

“This imperfect partnership is no longer enough to save Afghanistan,” said Moeed Yusuf, South Asia adviser at the U.S. Institute of Peace. He said President Obama’s plans to withdraw nearly 100,000 combat troops between next month and the end of 2014 require “an almost perfect coordination effort” with other elements of the administration’s strategy.

“I just don’t see how this is going to happen,” Yusuf said.

Conflicting accounts

Secretary of State Hillary Rodham Clinton and Defense Secretary Leon E. Panetta issued a joint statement of condolence over the deaths, and CIA Director David H. Petraeus telephoned his Pakistani counterpart Sunday. “Our side says they don’t know the facts,” said a second U.S. official, who also declined to discuss the matter on the record. “The facts are undoubtedly that somebody messed up on both sides.”

A former U.S. official who closely follows events in the region said the Pakistani army’s 11th Corps command near the western border was informed that coalition operations would take place Friday night and Saturday morning in the Maya area of Afghanistan’s Konar province. Maj. Gen. Athar Abbas, the chief Pakistani military spokesman, said in an interview Sunday that coalition forces “informed our military earlier, much earlier, that they will be conducting an operation there.”

Afghan security officials said Monday that the Special Operations mission was targeting training bases and hideouts of Taliban fighters. Insurgents there had regularly fired at a U.S. base in the area in the past, the officials said.

The Afghan officials said the coalition troops came under fire from the vicinity of the Pakistani bases, located in the Mohmand tribal areas, and they called in airstrikes in self-defense.

One senior Afghan police official said that after an initial gun battle, the insurgents retreated into a Pakistani post and began firing from there. “They started firing at the commandos, and they continued firing, so the air support had to come to their defense,” the official said.

The Pakistani defense official offered a sequence of events that differed in key aspects.

The Pakistani post, called Volcano, is clearly marked on grids shared with Afghan and coalition forces and flies the Pakistani flag. Its mission, the official said, is to prevent the return of Afghan insurgents that Pakistan has driven over the border. “We have repeatedly sensitized our friends [in Afghanistan] to this situation and asked their cooperation,” the official said.

Early Saturday, he said, Volcano “detected suspicious activity — sound and movement — in the vicinity. They are sitting there for the express purpose of stopping infiltration, so what do they do? They fire a few flares, a couple of mortar rounds and one or two bursts of heavy machine-gun fire in that direction.”

The Pakistani official added that “there was no return fire” from the ground. He dismissed suggestions by U.S. officials that the subsequent strike on Volcano and another post by U.S. attack helicopters and helicopter gunships was a case of mistaken identity provoked by Taliban forces in the area.

Even if the attack began that way, he said, “within a maximum of 10 or 15 minutes” the Americans should have known they were Pakistani military posts.

Partlow reported from Kabul. Staff writer Karin Brulliard in Islamabad, Pakistan, and special correspondents Sayed Salahuddin and Javed Hamdard in Kabul, Shaiq Hussain in Islamabad, and Haq Nawaz Khan in Peshawar contributed to this report.