Supporters of Pakistan Muslim League-Nawaz (PML-N) burn a US flag during a protest in Multan on November 28, 2011, against a NATO strike on Pakistan troops. Pakistan denied provoking NATO air strikes that killed 24 Pakistani soldiers and refused to accept expressions of regret over the cross-border attack that has inflamed US-Pakistani ties. AFP PHOTO/ S.S. MIRZA

A NATO airstrike along the Afghanistan–Pakistan border on Saturday that killed 24 Pakistani soldiers has once again inflamed U.S.–Pakistan tensions and called into question the future of the partnership.

The circumstances surrounding the strike are still unclear, and both NATO and U.S. Central Command have vowed to investigate the incident. Afghan and Western officials have said the airstrike was launched in response to firing from the vicinity of two Pakistani border posts. Pakistani military officials have denied those claims and said the NATO attack was unprovoked.

Islamabad responded swiftly to the incident by shutting down NATO supply lines that run through Pakistan into Afghanistan and demanding that all U.S. military personnel evacuate the Shamsi air base in Baluchistan province, which in the past facilitated the U.S. drone campaign in Pakistan’s tribal border areas. Islamabad had already demanded that the U.S. stop launching drones from Pakistani territory, and the eviction of the remaining dozen or so U.S. military personnel from the Shamsi air base seemed to be more of a symbolic rebuke of the U.S.

The military situation along the Afghanistan–Pakistan border is not black and white, and it is sometimes difficult to determine where enemy fire originates. Afghan insurgents on the Pakistan side are known to fire at NATO forces from areas close to Pakistan army posts, which leads to confusion about the precise location of the enemy. The ambiguous relationship between Pakistan’s military forces and some of the Afghan insurgents also lends itself to confusion over whether Pakistan is helping prevent militants from striking at coalition forces or turning a blind eye to their activities. The situation is unlikely to get any easier as NATO plans in 2012 to increase military operations in eastern Afghanistan along the border to shut down insurgent routes from Pakistan.

This tragic incident further highlights the strategic differences between the U.S./NATO coalition and Pakistan when it comes to the future of Afghanistan. Ties between the U.S. and Pakistan are destined to lurch from crisis to crisis unless and until the two sides can come to an understanding on the way forward in Afghanistan. Relations between Washington and Islamabad had just begun to recover from remarks made by recently retired chairman of the Joint Chiefs of Staff Admiral Michael Mullen in September alleging that the Haqqani network is an “arm” of Pakistani intelligence.

The incident will be a major setback to U.S.–Pakistan relations and will disrupt the two sides’ ability to cooperate in Afghanistan, but a radical break in relations is also probably not in the cards. The U.S. seeks continued engagement with Pakistan to help avoid a nightmare scenario in which a nuclear-armed nation of 180 million potentially succumbs to religious extremists. For its part, Pakistan needs aid from the U.S. and other Western lending institutions to sustain its economy and maintain its regional position.

The Obama Administration had hoped that the Bonn conference on Afghanistan, scheduled for next week, would help catalyze reconciliation efforts in Afghanistan. This incident and Pakistan’s harsh reaction (which includes threats to boycott the conference) have cast a pall over the Bonn process. Most doubted that the Bonn conference itself would result in any serious breakthroughs with regard to Afghan reconciliation, and this week’s events seem to make those prospects even dimmer.