The Long War in Pakistan

Progress in Afghanistan will be fleeting if it comes at the cost of creating more enemies for Islamabad in the border regions.

It took the destruction of almost 100 oil tankers and more than a week of suspended supplies before U.S. Ambassador to Pakistan Anne Patterson apologized for a Sept. 30 NATO helicopter incursion which killed three Pakistani soldiers. A U.S. Embassy statement late Wednesday said a joint investigation showed American pilots had mistaken the soldiers for Afghan insurgents they had been pursuing.

While Wednesday's apology may momentarily defuse anger in Islamabad, the prospects for a smoother working relationship are grim. That's because America's short-term objectives are at odds with the Pakistani government's long-term strategic interests.

Acrimony between hawks in Islamabad and Washington, where a new White House assessment sharply criticized Pakistan for being "unwilling to take action against al Qaeda and like-minded terrorists," has been growing for months. As an Obama administration official told the Journal earlier this week, "there are real challenges we have with Pakistan."

The stated American objective is to destroy al Qaeda and Taliban sanctuaries in the border regions of Pakistan and stabilize Afghanistan. Gen. David Petraeus, America's commander in Afghanistan, has hinted that his forces will do all they can to intercept and kill insurgents moving across the porous border between Afghanistan and Pakistan.

But there's a political angle to the General's mission: He needs tangible military success ahead of Congressional elections in November and the strategic review in December. That review will presumably focus on whether and how to gradually extricate the bulk of U.S. forces from Afghanistan in July next year. That goal has raised concerns in Islamabad and elsewhere that the Americans will leave prematurely.

Meanwhile, Pakistan is resisting American calls for all-out warfare against militants in and around North Waziristan. No one contests the fact that this mountainous area spread over roughly 5,000 square kilometers offers sanctuary for insurgents of all types—Afghans, Pakistanis, Arabs and Uzbeks. Several Pakistani militant groups—such as Lashkar-e-Taiba and Lashkar-e-Jhangvi—are also hiding there, under the protection of the Haqqani terrorist network. The question is what can be done.

Gen. Petraeus and the Obama administration view these militants as a significant source of instability in Afghanistan, where violence has tripled so far this year compared to the same period last year. Mr. Obama has suggested, according to Bob Woodward's new book "Obama's Wars," that the "safe haven" in Pakistan represents the biggest hurdle to a decisive victory in Afghanistan.

The Pakistani military establishment, however, believes that a head-on confrontation in North Waziristan will do more harm than good. It would not only antagonize dozens of wily tribes in the border region, but could also trigger a retaliation among Pakistan's militant networks, who have shown a growing willingness to turn their wrath on civilians.

Scores of militants from the vicious Tehreek-e-Taliban Pakistan and Lashkar-e-Jhangvi, crucial allies of al Qaeda in the border regions, have inflicted heavy human and material losses in roughly 50 suicide bombings so far this year. It is understandable that Pakistanis would not want to invite more. Targeted killings of liberal scholars such as Dr. Mohammad Farooq, a vocal critic of suicide bombings gunned down a week ago at his clinic, and continued bombing of girls schools underscore how violence plagues Pakistan.

The recent torching of fuel tankers thus inflamed an already combustible situation. Around two-thirds of all NATO cargo destined for Afghanistan passes through Pakistan, the shortest route for these consignments. Almost 6,500 trucks currently transport cargo from the Arabian Sea port of Karachi to Afghanistan, making it one of the largest cargo operations in recent decades. The Tehreek-e-Taliban claimed responsibility for these acts of arson but hard-line nationalists within the Pakistani security establishment may have prompted these attacks.

Continuing U.S. drone strikes, like the one that allegedly killed the German mastermind of a "Euro-terror plot," further complicate the relationship. The new rage against America is not restricted to the militants and their backers within the establishment. From right to left, almost every Pakistani is up in arms against the mounting pressure from Washington. Almost 27 drone strikes since early September and at least three border violations seem to have united most analysts, electronic media, columnists, politicians and members of civil society, who feel that the government must defend its sovereignty.

Reconciling the conflicting Pakistani and U.S. policy objectives therefore represents a formidable challenge. Most Pakistani analysts believe that Gen. Petraeus has shifted the focus of war from Afghanistan to their country in an effort to suck the Pakistan army into North Waziristan. But it is highly questionable whether a frontal assault by the Pakistan army on militants there would bring stability to Afghanistan. Pakistan has paid a high price for America's long and unpopular war across its border.

The U.S.-Pakistan relationship may not be at the breaking point yet. After all, Pakistan remains a crucial link in the U.S. strategy in Afghanistan. But Pakistan's own instability is also a source of concern to the administration. Washington has to remember that progress in Afghanistan will be fleeting if it comes at the cost of creating more enemies for Pakistan's weak and unpopular government in the border regions.

Mr. Gul heads the Centre for Research and Security Studies, Islamabad, and is the author of "The Most Dangerous Place" (Viking, 2010).