In a sign of growing concern over the deteriorating situation in Afghanistan and a renewed commitment to kill or capture al-Qaida's top leadership, the United States has launched military strikes across the border into Pakistan. These attacks signal U.S. frustration with Pakistan's efforts to battle Islamic militants in the border regions. They also risk alienating Pakistan's military and undermining its civilian government.

There has been rising concern over the deterioration of security in Afghanistan. It is estimated that nearly 1,500 Afghan civilians were killed in the first eight months of 2008, a death toll 39 percent higher than the previous year.

Adm. Mike Mullen, chairman of the U.S. Joint Chiefs of Staff, has confessed that he is not convinced the U.S. is winning in Afghanistan. The top NATO commander in Afghanistan said he needs as many as 15,000 more troops to strengthen the 71,000 foreign soldiers already on the ground — and that is on top of 5,000 U.S. troops already scheduled to deploy.

Convinced that al-Qaida and remnants of the Taliban, which are leading the resistance to the government of President Hamid Karzai in Kabul, are operating from sanctuaries in the border areas of Pakistan, the U.S. has stepped up its attacks in those areas, with missile strikes from unmanned aircraft and raids by U.S. troops. The U.S. claims it is attacking Taliban leaders; Pakistan says civilians are among the casualties. Reportedly, Pakistan's military has ordered its troops to open fire against U.S. forces if they come across the border again.

The raids are an invasion of sovereignty and offend Pakistani sensitivities. Pakistan's officials insist that they are doing all they can — more than 100,000 troops have been deployed to the region — and that the strikes fuel religious extremism in the country. The anger that is being unleashed and the failure of the government in Islamabad to prevent attacks by a so-called ally in the war on terror undermine the legitimacy of the government and could be contributing to an Islamic fundamentalist backlash. This in a state with a nuclear arsenal.

U.S. military commanders are not convinced that Islamabad is doing all it can to strike against militants in the border regions, who enjoy the sympathies of local tribal leaders. Previous offensives against the groups failed, embarrassing Pakistan's military, and resulted in agreements in which the military agreed to back off in exchange for the militants' halting their attacks within Pakistan itself.

The situation is further complicated by the transition back to civilian leadership in Islamabad. Former President Pervez Musharraf was forced to resign earlier this year and was replaced by Mr. Asif Ali Zardari, widower of Mrs. Benazir Bhutto, who was assassinated last year while campaigning for elections. Mr. Zardari is not a popular figure, and he must court both the public and the military.

The cross-border raids make Mr. Zardari look weak and turn substantial portions of Pakistan's population against him: Islamic groups that back the Taliban, nationalists who consider the raids a violation of their sovereignty, and ordinary citizens who fear the attacks will trigger another backlash of militant violence within Pakistan.

Equally important, the raids undermine Mr. Zardari's authority with the military, an institution that sees itself as the embodiment of Pakistan's sovereignty. In the past, a weak civilian government invited intervention by the military. It can only be hoped that the institution is still smarting from the rebuke administered to Mr. Musharraf when he was forced to leave office. If, however, the perceived humiliation continues, the military may be once again forced to act.

The danger of course is that the U.S. need for action against the Taliban may force it to defer to the military. The U.S. cannot afford to ignore the institution that has the most experience combating Islamic forces. Yet there are real doubts about the ability of the military to find the militants on their own. Close coordination and cooperation is needed.

Here too exists the danger of undercutting Mr. Zardari. A military that feels it has its own relationship with the U.S. is a military that is too strong. Civilian authority in Pakistan must be strengthened. The U.S. must work through the government in Islamabad, even though doing so may be slow and frustrating.

Other countries, such as Japan, should help to strengthen civilian supremacy through economic development projects that build national capacity for governance and improve the lives of ordinary Pakistanis. This will build a foundation for civilian governance, which will in turn undermine the appeal of Islamic militancy in Pakistan.