Three weeks ago, 24 Pakistani soldiers dug in trenches along the Afghan-Pakistani border were accidentally killed by NATO aircraft during one of the many counterinsurgency missions that American and Afghan troops have undertaken over the past year. Except on this particular nighttime raid, the precision and professionalism that have become hallmarks of the coalition’s military campaign in Afghanistan were lost, tragically ending the lives of over two dozen men.

The Pakistani military and government, which have had a frosty relationship with the United States for most of the year, responded angrily. The Pakistani embassy in Washington went so far as to tell reporters that the NATO operation was a deliberate act aimed at loosening the morale of the Muslim nation — a viewpoint that, while conspiratorial, may be acceptable given Islamabad’s roller coasty partnership with the Americans.

Sensing that another fallout in American-Pakistan relations would hurt the NATO war effort in Afghanistan, the Department of Defense called their Pakistani counterparts and told them that a transparent and factually based investigation would be implemented. That Pentagon study is now out and to the consternation of Western military officials, it looks like the Pakistanis may not have been wrong in all of their assertions.

Although the final report has not been made public, the Defense Department released a press statement briefly touching upon its most important findings. In sum, the investigation concluded that NATO was perfectly within its right to return fire in self-defense but the coordinates that were given to Pakistani soldiers in the area turned out to be wrong.

The investigating officer found that American forces, given what information they had available to them at the time, acted in self-defense and with appropriate force after being fired upon. Nevertheless, inadequate coordination by American and Pakistani military officers operating through the border coordination center — including our reliance on incorrect mapping information shared with the Pakistani liaison officer — resulted in a misunderstanding about the true location of Pakistani military units.

The study is not a perfect inquiry. Out of protest, the Pakistani military refused to cooperate with the Pentagon’s investigation, which lead investigator Brigadier General Stephen Clark acknowledged was a significant setback in uncovering all of the facts.

The findings are certain to draw condemnation from the Pakistanis who continue to feel insulted by what they view as Washington’s lack of appreciation for the thousands of military and civilian casualties that they have suffered in the fight against terrorism since 2001. General Athar Abbas, the chief Pakistani military spokesman, quickly indicated that his colleagues rejected the report’s conclusions.

The completion of the inquiry leaves the Obama Administration with a difficult decision to make. Does the president “swallow American pride” and formally apologize for NATO’s part of the responsibility or will he continue to express regret over the incident without offering that apology?

At least for the time being, the White House and the State Department have not budged from their original position. A State Department spokesman attempted to take responsibility for NATO’s infractions at a press briefing after the report’s release, all the while punting questions on apologizing.

Now that US/NATO forces are indeed held liable for at least part of the border incident, the administration should in fact reverse its previous stance, privately and publicly making it clear that anyone on the American side who was part of the problem will be dealt with accordingly.

President Obama and Secretary of State Hillary Clinton have been on the phone for weeks with Pakistani Chief of Army Staff General Ashfaq Pervez Kayani and the Pakistani foreign minister, Hina Rabbani Khar, trying to rebuild a tattered relationship. Kayani has reestablished contacts with NATO commander General John R. Allen, a good start to making sure that a deadly accident like the one that occurred on November 24 does not happen again. But neglecting to say “I’m sorry,” even as the Pentagon investigation details that NATO did in fact make mistakes, will give the Pakistanis a greater reason to doubt the United States as committed partners in the region.

The reality is that as long as the United States are engaged with tens of thousands of troops in Afghanistan, Washington needs Pakistan’s help — whether or not Pakistan has been truly forthcoming in battling militancy on its own soil. Absent cordial relations between the two countries, NATO commanders can expect Islamabad to continue closing down supply routes that go into Afghanistan — forcing the coalition to either spent millions more airlifting supplies or putting them increasingly into the pockets of Central Asia’s autocratic regimes.

Pakistan may be a double faced partner right now but imagine how much worse NATO’s experience in Afghanistan would be without a measurable level of Pakistani complicity. Sometimes in war, a nation does not get to choose its allies. Pakistan is one such nation — a pain to deal with but necessary for a smooth NATO conclusion to the war across the border.