Resolution of the dispute also bandages a relationship with Pakistan that will be crucial in stabilizing the region. The ties have been torn in the past year and a half by everything from a CIA contractor who killed two Pakistanis to the unilateral U.S. raid on Osama bin Laden's Pakistan compound.
But the accord carries risks for both governments — threatening to make Pakistan's already fragile civilian leadership look weak and subservient to the United States while offering fodder to Republicans including presidential candidate Mitt Romney who contend that President Barack Obama says "sorry" too easily.
The first trucks carrying NATO goods should move across the border on Wednesday, U.S. officials said. It could take days to ramp up supplies to pre-attack levels, but around two dozen impatient truck drivers celebrated the news in a parking lot in the southern city of Karachi by singing, dancing and drumming on empty fuel cans.
"We are sorry for the losses suffered by the Pakistani military," Clinton said, recounting a telephone conversation she had with Pakistani Foreign Minister Hina Rabbani Khar concerning the deaths that led Pakistan to close the supply routes. "I offered our sincere condolences to the families of the Pakistani soldiers who lost their lives. Foreign Minister Khar and I acknowledged the mistakes that resulted in the loss of Pakistani military lives."
"I am pleased that Foreign Minister Khar has informed me that the ground supply lines into Afghanistan are opening," Clinton added in her statement.
It marked the first time any U.S. official formally apologized for the deaths, a step hotly debated within the Obama administration and one demanded by Pakistan before it would reopen the supply routes. Pakistani lawmakers also wanted Washington to halt all air strikes in the country and stop shipping weapons and ammunition to Afghanistan through Pakistani airspace, demands the U.S. has ignored. Negotiations stumbled at one point over transit fees Pakistan sought to charge.
The November incident was the deadliest among the allies in the decade-long fight against al-Qaida and other extremist groups along the Afghan-Pakistani frontier.
An American investigation found that Pakistani forces fired first and U.S. soldiers responded in self-defense. It blamed bad maps, poor coordination and Islamabad's failure to provide the locations of its borders for the failure to determine if Pakistani forces were in the area. Pakistan argued that its troops shot at militants who were nowhere near coalition soldiers, and accused the U.S. of launching a deliberate attack.
The breakdown of the U.S.-Pakistani partnership arrived at an awful time, only weeks after Clinton and CIA Director David Petraeus went to Islamabad to patch up the relationship and secure a Pakistani commitment to snuff out support given by its intelligence services to the Taliban — support that Washington sees as a threat to the Afghan war effort.
The Obama administration, in an election year, expressed regret for the deaths but dug in its heels over the word "sorry," fearful it might open the president to criticism from Republicans already critical of Pakistan's links with militants fighting in Afghanistan.
It is also unclear what the apology will mean for the U.S. call for Pakistan to crack down on the militant Haqqani network, which is believed to use Pakistan as a rear base for attacks on American troops in Afghanistan.
Having titled his campaign book, "No Apology," Romney accuses Obama of having gone "around the world and apologized for America." The accusation refers to Obama's trip to Cairo early in his presidency, when he sought to repair U.S. relations with the Muslim world. Clinton's remarks made no reference to an "apology," though she did use the word "sorry."
Obama made no comments about Pakistan on Tuesday, leaving Clinton's statement as the only official U.S. explanation of the agreement. It was released just as Pakistani civilian and military leaders were meeting to discuss whether to reopen the routes, and there was no confirmation from Islamabad of a decision for more than two hours.
"The main thing is that a superpower has acknowledged our principled stance, and they have shown flexibility," said Information Minister Qamar Zaman Kaira, speaking in Urdu. "It was not the issue of money. It was the issue of our sovereignty," he said, adding that American authorities assured Pakistan there would be no repeat of the incident.
The prime minister's office said the government reopened the supply lines in and out of Afghanistan to help its northern neighbor's "transformation process" more than a decade after bin Laden used the country to launch the Sept. 11, 2001, terrorist attacks and the U.S. responded by helping overthrow the Taliban.
It stressed that reopening the supply lines would help the U.S. pull out of Afghanistan sooner, saying the transition was in "Pakistan's interest." The statement sought to head off the inevitable political backlash in a country where anti-American sentiment is rife and the United States is often blamed for internal problems.
Still, Pakistan's more conservative political groups rejected the decision. Amirul Azim, a top leader of Pakistan's radical Jamaat-e-Islami party, said, "The main thing is that we should not reopen the NATO supply route, and we should isolate ourselves from this so-called war against terrorism."
And the fallout could hurt Pakistan's civilian government, which was re-established four years ago after a history of military coups. It has struggled to assert itself against the powerful Pakistani army and hardline Islamist religious leaders and politicians, who will likely point to the several parliamentary demands the U.S. ignored, including the call for an "unconditional apology" for the attack. Washington mentioned mistakes on both sides.
Clinton said Pakistan wouldn't charge any new transit fee and the reopening would help the U.S. draw down its forces in Afghanistan "at a much lower cost."
The U.S. government has never paid transit fees directly. Pakistan charges companies $250 per truck for transit, and the U.S. accounts for those fees in its contracts with those companies, so it pays indirectly. During negotiations Pakistan had asked for a flat fee of up to $5,000, but Washington offered extensive road construction projects to sweeten the deal.
With the supply lines closed, the U.S. has been forced to use more costly transportation routes through Russia and Central Asia. Defense Secretary Panetta had estimated the cost at an extra $100 million a month, warning that it could get more expensive as the U.S. started to withdraw equipment in advance of the 2014 troop drawdown in Afghanistan.
That estimate would mean the lengthy standoff cost U.S. taxpayers some $700 million, and denied Pakistan's revenue-starved government millions of dollars in transit fees.
The total could be more.
The Pentagon asked Congress last week for approval to transfer $2.1 billion from other funds to cover costs largely resulting from the closure of the Pakistan supply routes.
Three separate transfers totaling $1.7 billion covered increased fuel and transportation costs for the Army. A fourth transfer of about $370 million was for the Air Force, which had to increase the transportation of supplies by air in part to compensate for the shutdown of the ground routes through Pakistan. The budget request did not specify how much of the $370 million was related to the Pakistan problems and how much was just additional support for the war.
Panetta said Tuesday he welcomed Pakistan's decision.
"We remain committed to improving our partnership with Pakistan and to working closely together as our two nations confront common security challenges in the region," he said.
According to the Pentagon, the agreement should free hundreds of millions of dollars in U.S. counterterrorism money for Pakistan that Washington suspended last year.
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