Nonstop crises between the United States and Pakistan this year have fueled tensions within the Obama administration over what kind of relationship the two countries should have and who should be in charge of it.

The State Department has long smarted over the preeminence of military and intelligence priorities, which seems to leave diplomacy in a distant third place. The result, diplomats say, is that there is little goodwill to cushion blows such as the U.S. airstrike last month that left two dozen Pakistani soldiers dead along the Afghanistan border.

More than a week after the attack, President Obama called Pakistan’s president on Sunday to say that the deaths were “regrettable,” stopping short of an apology that many in Pakistan have called for.

The airstrike has cast a shadow over a major diplomatic gathering Monday in Bonn, Germany, that the administration hoped would help facilitate plans to wind down the Afghanistan war. Pakistan has said that it will not attend the meeting, which brings together more than 100 countries and international organizations and whose agenda includes regional and Afghan development and peace talks with the Taliban.

Secretary of State Hillary Rodham Clinton, who will lead the U.S. delegation, unsuccessfully appealed for a change of heart in a telephone call Saturday to Pakistani Prime Minister Yousuf Raza Gilani.

The U.S.-Pakistan breach has also set back Obama administration attempts to improve the brittle relationship between Pakistan and Afghanistan. Afghan President Hamid Karzai told Germany’s Der Spiegel magazine on the eve of the Bonn meeting that he thought Kabul’s closest neighbor was trying to sabotage the possibility of peace negotiations.

Many of Clinton’s diplomatic troops see the border clash as the latest example of a disconnect between what one State Department official called short-term security objectives and long-term diplomatic goals.

The global nature of the war against al-Qaeda and other terrorist groups has expanded the presence of U.S. military and intelligence personnel into countries and American embassies to the point where they often outnumber and vastly outspend their civilian counterparts, whose portfolios now involve far more security-related work than they trained for.

“In a lot of ways, diplomacy is this historical anachronism,” said the official, who spoke of diplomatic concerns only on the condition of anonymity.

The imbalance is particularly acute in Pakistan, where the Obama administration is trying to prop up the weak civilian government while lavishing funds and attention on the recalcitrant military and conducting counterterrorism operations through an extensive intelligence presence and drone attacks.

Although they share Pentagon and CIA impatience with and mistrust of the Pakistanis, American diplomats said appearances and perceptions could be as important as actions in pursuing U.S. goals — particularly because one of them is to convince a strongly anti-American public that the United States wants to help, not harm, Pakistan.

The U.S. response to the airstrike is a prime example, diplomats said. In the nine days since the episode, Pakistani and U.S. accounts have differed over key details, including who fired first and how long the attack lasted. Results of a Pentagon investigation are not due until Dec. 23.

U.S. Ambassador Cameron Munter has said that an apology from Obama would help assuage Pakistani fury over the airstrike. The Pentagon and the White House have insisted on waiting for the investigation to run its course.

Regardless of who was at fault in the border clash, “this whole sovereignty thing is so strong because we do precisely what we want in their territory and this drives them crazy,” said another State Department official, who spoke on the condition of anonymity. “Knowing they can’t do anything about it drives them even more crazy. When we get in a hurry, we don’t even bother to fake it.”

Far more than his predecessors, Munter has questioned the timing of drone attacks — including in the immediate aftermath of previous crises over the fatal shooting of two Pakistanis by a CIA contractor in January and the U.S. raid that killed Osama bin Laden in May — and asked the White House to clarify whether he has a veto over specific raids, according to current and former White House and State Department officials.

For their part, the Defense Department and the CIA have their own complaints — with each other and with the U.S. Embassy, which they sometimes see as coddling a dysfunctional Pakistani government and interfering with core U.S. counterterrorism objectives.

A five-year, $7.5 billion economic aid package passed in 2009 was supposed to anchor the relationship more firmly on the civilian side.

“But since January, the formula has been reversed,” said Vali Nasr, a Tufts University professor who until this year held a senior State Department position specializing in Pakistan.

“The security, counterterrorism and now Afghanistan is actually making the civilian relationship almost impossible, or irrelevant, let me put it that way,” Nasr said.

Drone attacks and incidents such as the airstrike last month have bolstered the Pakistani military’s power and image as the nation’s bulwark against outside aggression and made the United States so unpopular that Pakistani government and civil society leaders fear being seen as too close to American diplomats.

Until his retirement in September, Adm. Mike Mullen, who was chairman of the Joint Chiefs of Staff, was the most public face of the bilateral relationship. Mullen’s trips to Pakistan for face-to-face meetings with Pakistan’s army chief, Gen. Ashfaq Kayani, were far more frequent than Clinton’s visits with the civilian authorities.

When an exasperated Mullen publicly accused Pakistan’s military of supporting Afghan insurgent groups in congressional testimony just before leaving office, some State Department officials said they felt blindsided.

On a subsequent visit to Pakistan in October, Clinton insisted on leading a delegation that included CIA Director David H. Petraeus and Mullen’s replacement, Gen. Martin E. Dempsey.

But the State Department’s efforts to assert at least the appearance of control over U.S. policy are regularly undermined by a steady stream of congressional visitors to Pakistan who “all want to visit Kayani,” an administration official said. “They don’t want to talk to their civilian counterparts” in Pakistan’s Parliament, “and they only want to stay a few hours,” the official said.

Retired Maj. Gen. Mahmud Ali Durrani, a former national security adviser to Gilani and Pakistani ambassador to the United States, agreed with that reality and the impression it leaves in Pakistan. “You look at the visitors from Washington,” Durrani said. “They would go and spend time with the president, then most of the serious discussions they had with the army chief.”

“In my view,” he said, “there is one and only one issue” between Pakistan and the United States, “and that is counterterrorism. And that is in the lap of the security establishment. So that, in itself, is a problem.”

Brulliard reported from Islamabad, Pakistan.