The Obama administration scrambled to halt a sharp deterioration in its troubled relationship with Pakistan on Wednesday, offering Pakistani officials multiple apologies for a helicopter strike on a border post that killed three Pakistani soldiers last week. But even as the White House tried to mollify Pakistan, officials acknowledged that the uneasy allies faced looming tensions over a host of issues far larger than the airstrike and the subsequent closure of supply lines into Afghanistan. American pressure to show progress in Afghanistan is translating into increased pressure on Pakistan to crack down on terrorist groups. It is also running up against Pakistans sensitivity about its sovereignty and its determination to play a crucial role in any reconciliation with the Taliban. American and NATO officials said privately that the Pakistani governments closing of a crucial border crossing might have made it easier for militants to attack long lines of backed-up tanker trucks carrying fuel through Pakistan to Afghanistan to support the American war effort. Still, the unusual apologies, officials and outside analysts said, were intended to clear away the debris from the explosive events along the border, in hopes of maintaining Pakistani cooperation. We have historically had astonishing sources of resilience in our relations with Pakistan, said Teresita Schaffer, a South Asia expert at the Center for Strategic and International Studies. One should not too quickly assume were in a breakpoint. But having said that, the time were in right now, the intensity of anti-American feeling, the antipathy of militants, all of these things make new crises a little more complicated to get through than the old ones were. The overall commander of forces in Afghanistan, Gen. David H. Petraeus, has been pulling out all the stops aggressively using the American troop buildup, greatly expanding Special Operations raids (as many as a dozen commando raids a night) and pressing the Central Intelligence Agency to ramp up Predator and Reaper drone operations in Pakistan. He has also, through the not-so-veiled threat of cross-border ground operations, put pressure on the Pakistani Army to pursue militants in the tribal areas even as the army has continued to struggle with relief from the catastrophic floods this summer. The fragility of Pakistan and the tentativeness of the alliance were underscored in a White House report to Congress this week, which sharply criticized the Pakistani military effort against Al Qaeda and other insurgents and noted the ineffectiveness of its civilian government. American officials lined up to placate Pakistan on intrusions of their sovereignty. General Petraeus offered Pakistan the most explicit American mea culpa yet for the cross-border helicopter strikes, saying that the American-led coalition forces deeply regret the tragic loss of life. Anne W. Patterson, the American ambassador to Pakistan, quickly followed suit, calling Pakistans brave security forces an important ally in the war. Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, offered a private, but official, apology to Pakistans military chief, Gen. Ashfaq Parvez Kayani, in a telephone call on Wednesday afternoon. Both American and Pakistani officials said that they expected that Wednesdays apologies would be effective, at least in the short term, and that Pakistan would soon reopen the border crossing at Torkham, a supply route for the NATO coalition in landlocked Afghanistan that runs from the port of Karachi to the Khyber region. The Pakistani government closed that route last week to protest the cross-border strikes. Its obvious that the situation right now aint good, said a senior NATO official, who agreed to speak candidly but only anonymously. The best thing we could do is to strip away as many of the relatively smaller things as possible so we can focus on the big issues. And crazy as it may seem, the border crossing is a relatively small issue, compared to the others. Those other issues were flagged in the latest quarterly report from the White House to Congress on developments in the region. The assessment, first reported in The Wall Street Journal on Wednesday, takes aim at both the Pakistani military and the government. For instance, the Pakistani military continued to avoid military engagements that would put it in direct conflict with Afghan Taliban or Al Qaeda forces in North Waziristan, the report said. It also painted Pakistans president, Asif Ali Zardari, as out of touch with his own populace, a disconnect which the report said was exacerbated by Mr. Zardaris decision to travel to Europe despite the floods. The overall Pakistani response to the catastrophic floods this summer, the report said, was viewed by Pakistanis as slow and inadequate. Frustration with Pakistan is growing in the United States in part because were living in the post-Faisal Shahzad era, said Daniel Markey of the Council on Foreign Relations, referring to the Pakistani-American who was sentenced to life in prison on Tuesday for the attempted Times Square bombing. Mr. Markey said that tensions among counterterrorism officials had also mounted because of the unspecified threats of terrorist attacks in Europe. Frustration has really mounted, so the drumbeat is getting louder, he said. Making things worse, the administration is expected to brief Congressional officials on an Internet video, which surfaced last week, that showed men in Pakistani military uniforms executing six young men in civilian clothes, underscoring concerns about unlawful killings by Pakistani soldiers supported by the United States. A prominent House Democrat warned on Wednesday that American aid to Pakistan could be imperiled. I am appalled by the horrific contents of the recent video, which appears to show extrajudicial killings by the Pakistani military, Representative Howard L. Berman, a California Democrat who leads the House Foreign Affairs Committee, said in a statement. The failure of Pakistani officials to punish those responsible could have implications for future security assistance to Pakistan, he said. A joint Pakistan-NATO inquiry on the helicopter strike concluded on Wednesday that Pakistani border soldiers who initially fired on NATO helicopters were simply firing warning shots after hearing the nearby engagement and hearing the helicopters flying nearby, said Brig. Gen. Timothy M. Zadalis, a NATO spokesman, in a statement. This tragic event could have been avoided with better coalition force coordination with the Pakistani military, he said.(NYT)