— As thousands of angry Afghans flung rocks at NATO’s largest military base in Afghanistan on Tuesday, American officials sought to quell a widening furor over what they said was the accidental incineration by U.S. military personnel of copies of the Islamic holy book. 
 
 The protests erupted early Tuesday after Afghans working at Bagram air base told local residents that a number of copies of the Koran had been burned. When they carried out the charred pages, waving them in the air, the crowd grew larger and more defiant. 
 
 Among those chanting “Long live Islam” and “Death to America” were some of the 5,000 Afghans who have worked inside the base for years. Gen. John R. Allen, the top U.S. commander in Afghanistan, was quick to express contrition for the incident, which officials worried could incite violence across the country. 
 
 U.S. officials said the books were mistakenly sent with a pile of trash for disposal before several Afghans identified them. Although the initial protests were concentrated largely around the Bagram base, some of the charred Koran remains were sent promptly to Kabul, where President Hamid Karzai and other top Afghan officials will decide how to respond to the incident. 
 
 “These people must be punished,” said Qari Ghulam Mustafa, a top religious official from Parwan province, where Bagram is located. He carried a stack of 10 blackened Korans on his lap as he and others traveled to the capital in a white hatchback. He said nearly 100 more publications were damaged. 
 
 “If the Americans ever deny that they did this, we will show them these pages,” said Mullah Abdul Rahim Shah Agha, the head of the Parwan ulema council, or Muslim clerical body. 
 
 The apologies from Allen and top Obama administration officials were among the most profuse of the decade-long war. But there was no immediate indication that they would calm the kind of unrest that has turned explosive in the past, notably in April, when deadly protests broke out over a case of Koran-burning in Florida. 
 
 “When we learned of these actions, we immediately intervened and stopped them,” Allen said in a statement. “We are taking steps to ensure this does not ever happen again. I assure you . . . I promise you . . . this was NOT intentional in any way.” 
 
 The United States faces an enormous challenge in withdrawing its troops over the next two years while attempting to protect hard-won gains and facilitate a delicate peace process between the Afghan government and Taliban insurgents. With so little margin for error, the incident Tuesday could threaten the relationship on which U.S. military and diplomatic strategies depend. 
 
 U.S. and Afghan officials expressed concern about the prospect of more violent reaction in coming days. 
 
 The U.S. Embassy in Kabul warned American citizens, “Past demonstrations in Afghanistan have escalated into violent attacks on Western targets of opportunity.” 
 
 The incident also could complicate relations between NATO forces and those Afghans who perform a variety of nonmilitary functions on bases. The hundreds of Bagram employees who were among the protesters will have to decide whether to leave their jobs or continue working while disguising their antipathy. 
 
 “The people who do this are our enemies,” said a 27-year-old who has worked at a warehouse on the base for two years. “How could I ever work for them again?” 
 
 Another Bagram employee who joined the protest said, “Whoever goes back to work will be killed. They’ll think of us as traitors.” The workers declined to give their names for fear of reprisals. 
 
 More than 3,000 people were involved in the protests Tuesday. Afghan and Western security forces blocked roads leading to the base and instructed local employees to stay home. But when they heard about the incident, the workers arrived at the base’s front gate in droves. 
 
 Rumors about the incident — and American motives — circulated through the crowd. In Kabul, 35 miles to the south, even top Afghan officials struggled to understand what had happened. 
 
 Gen. Ahmad Amin Naseeb, director of the Afghan army’s religious and cultural affairs department, said he had been told “that the international troops have burned and thrown copies of the Koran into the dustbins.” 
 
 In his second statement of the day, Allen announced that all NATO forces in Afghanistan would complete training in the proper handling of religious materials by March 3. 
 
 NATO said religious materials, including Korans “identified for disposal,” were collected at the Parwan Detention Facility, a prison next to the base, and “were inadvertently taken to an incineration facility at Bagram airfield” Monday night. 
 
 A senior U.S. military official said the Korans were removed from the prison library because they had radical or inflammatory messages scrawled in them. A Western official, speaking on the condition of anonymity, told the Associated Press that the texts were charred but that none were destroyed. 
 
 Proper treatment of the Koran is a highly sensitive issue for Muslims across the world, including in Afghanistan, where international troops are fighting to defeat the militantly Islamist Taliban in a war that has entered its 11th year. Experts in Islam say copies of the Koran should be buried or released in flowing waters if they need to be disposed of, but religious leaders in Afghanistan said Tuesday that local practice is not to dispose of the texts at all. 
 
 In Washington, White House spokesman Jay Carney echoed Allen’s apology, saying: “We apologize to the Afghan people and disapprove of such conduct in the strongest possible terms. This deeply unfortunate incident does not reflect the great respect our military has for the Afghan people. It’s regrettable.” 
 
 Staff writer Greg Jaffe in Washington and special correspondents Sayed Salahuddin and Walid Fazly in Kabul contributed to this report. ||||| In the course of one week, the burning of copies of the Koran by U.S. military personnel in Afghanistan has set off a deadly chain of events that has not only inflamed tensions but possibly exposed a crippling weakness in the American strategy to wind down the war. 
 
 The emerging U.S. strategy in Afghanistan is built around plans to replace large NATO combat formations with small teams of advisers who will live and work alongside their Afghan partners. 
 
 But the killing of two high-ranking NATO officers by an Afghan security official — and the subsequent decision by the top NATO commander in the country to recall his personnel from top Afghan ministries — has spurred doubts about whether Afghan security forces can be relied upon to provide for the protection of their Western partners. The consequences of that erosion of confidence, former U.S. officials and analysts say, could be devastating. 
 
 “If the trust, ability and willingness to partner falls apart, you are looking at the endgame here,” said Mark Jacobson, who served until last summer as the NATO deputy senior civilian representative in Kabul. 
 
 The killing of the U.S. officers on Saturday occurred two days after a man wearing an Afghan army uniform fatally shot two American troops in eastern Afghanistan, the latest in a string of incidents in recent months in which local security forces have turned against NATO personnel. 
 
 Some of the killings have been perpetrated by Afghan troops whose loyalties lay with the Taliban. But, in most cases, the attacks have been the result of tensions between U.S. forces and Afghans who felt as though they had suffered an insult to themselves or their faith. 
 
 On Sunday, Afghan President Hamid Karzai, who initially responded to the Koran burnings with outrage, sought to stem the latest wave of violence by issuing a plea for calm and blessing the withdrawal of NATO advisers from his ministries as a justifiable measure. 
 
 But protests continued, including in the northern city of Kunduz, where Afghan demonstrators opened fire and tossed a grenade at a U.S. base, wounding seven American troops. The Afghan defense and interior ministers canceled a long-planned trip to Washington to focus on curbing the violence, which has claimed 25 Afghan lives. 
 
 “We remain committed to a partnership with the Afghan government and people,” the U.S. ambassador to Kabul, Ryan C. Crocker, told CNN on Sunday, promising that American service members and civilians would continue to work with their Afghan allies. 
 
 For now, though, much of the cooperation between U.S. advisers and their Afghan partners is on hold. And even though the decision to withdraw the advisers is probably temporary, it is not clear how U.S. troops will be able to reestablish trust with Afghan security forces. 
 
 “This is not going back to business as usual,” an Army officer who works as an adviser in Kabul said Sunday. “The threat is still higher than normal.” 
 
 Once advisers return to the ministries, the officer said, some will probably have to shorten their visits, instead of remaining there for six- to 10-hour shifts, to reduce risks. 
 
 Senior Obama administration officials have sought to reassure a war-weary American public that the NATO combat mission in Afghanistan would draw to a close by the middle of next year. These officials have implied that the change to an advisory mission would not only mean fewer U.S. service members in Afghanistan, but also less risk for the noncombat troops who remain behind. 
 
 Military experts, however, say that the smaller U.S. advisory force might be more exposed to fratricidal attacks than conventional military units. Such attacks — which were exceptionally rare in Iraq — often stem from a cultural chasm between U.S. and Afghan troops. 
 
 Carter Malkasian, who served as a State Department adviser in southern Afghanistan’s Helmand province in 2010 and 2011, said one way to mitigate that risk is for advisers to build closer relationships with their Afghan partners. But the risk will always be there. 
 
 “The most effective advisers will be with their Afghans all the time, and that certainly does involve additional risk,” Malkasian said. 
 
 Unlike a typical infantry platoon, which consists of more than 35 heavily armed soldiers, the advisers work in teams of as few as a dozen troops. Some military and civilian advisers working in Afghanistan said Sunday that the risks associated with their jobs were still manageable and that they believed that they would soon be able to return to their work. 
 
 “I hope [the ban] is lifted soon,” said a State Department adviser working at a remote outpost in eastern Afghanistan. “Maybe I am complacent. I know we face all kinds of threats, but we have a job to do.” 
 
 Current plans call for the U.S. force in Afghanistan to fall from a peak of 100,000 troops to about 68,000 by the end of the summer. Further reductions are likely later this year and in 2013. All NATO combat troops are expected to be withdrawn by the end of 2014. 
 
 In an article in the upcoming issue of Foreign Affairs, Malkasian and Kael Weston, who served a multiyear stint as an adviser in southern Afghanistan, estimated that NATO could hold off the Taliban and keep the Afghan government and security forces functioning with as few as 25,000 advisory troops. 
 
 The Afghans would rely on the NATO advisers to call in airstrikes if their position was about to be overrun by a larger Taliban force. The advisers would ensure that their Afghan partner units were receiving ammunition, food and fuel from their headquarters. The Westerners also would help control the most damaging and overt acts of corruption. 
 
 To be effective, these troops would have to live without large American bases, expensive dining facilities and intensive quick-reaction forces. 
 
 “The more willing advisers are to accept risk,” Malkasian said, “the more effective they will be.” 
 
 Special correspondent Javed Hamdard in Kabul contributed to this report.
– Afghanistan has roiled with violence for the past week over the Koran burnings at Bagram, leading to questions of whether the American exit strategy will actually work as planned. The US, Britain, Germany, and France temporarily removed hundreds of advisers from Afghanistan over the weekend in the wake of several retaliatory attacks—four US troops have been killed by Afghan comrades since the protests began—and some fear that Afghan security forces will not be able to protect the few Western advisers who will remain in Afghanistan after the withdrawal is complete. One adviser says he expects that upon their reinstatement, shifts will have to be shortened for the advisers' protection. Recent months have seen a number of incidents involving Afghan security forces turning on NATO personnel—and only some out of those incidents arose out of loyalty to the Taliban, the Washington Post notes. Most involved Afghan troops who felt insulted in some fashion, such as after the Koran burning came to light, and military experts think there could be an even higher risk of such attacks after the military withdrawal. A former US Army Ranger tells the Wall Street Journal that Americans are wary of sending advisers "to a country where those trainers and advisers are liable to be targeted by the very people they are training and advising."