The Taliban claimed responsibility for the Interior Ministry attack, saying it was retaliation for the Quran burnings.

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KABUL, Afghanistan — A gunman killed two U.S. military advisers with shots to the back of the head Saturday inside a heavily guarded ministry building, and NATO ordered military workers out of Afghan ministries as protests raged for a fifth day over the burning of copies of the Quran at a U.S. military base.

The Taliban claimed responsibility for the Interior Ministry attack, saying it was retaliation for the Quran burnings, after the U.S. officers — a lieutenant colonel and a major — were found dead on the floor of an office that only people who know a numerical combination can enter, Afghan and Western officials said.

The top commander of U.S. and NATO forces, Gen. John Allen, recalled all international military personnel from the ministries, an unprecedented action in the decadelong war, highlighting the growing friction between Afghans and their foreign partners at a critical juncture.

The U.S.-led coalition is trying to mentor and strengthen Afghan security forces so they can lead the fight against the Taliban and foreign troops can go home. That mission, however, requires a measure of trust at a time anti-Western sentiment is at an all-time high.

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The escalating tension prompted apologies for the Quran burning from President Obama and several top U.S. defense officials. But demonstrations continued unabated Saturday, even before U.S. officials reported that an Afghan security officer had killed the two American advisers in one of Kabul’s most important and most impenetrable ministries.

The two men, whose names were not released, were shot while working at their desks.

Within hours of the attack, Allen recalled all coalition advisers from Afghan ministries, citing “obvious force-protection reasons.”

The order applies to service members operating under the NATO flag, including members of the 49 coalition countries, and other U.S. military personnel who are separate from the NATO chain of command.

There are at least several hundred advisers embedded in almost every department of the security ministries, but a NATO spokesman would not give a number. The advisers work on everything from logistics and weapons training to strategic planning.

Afghan Defense Minister Gen. Abdul Rahim Wardak called U.S. Defense Secretary Leon Panetta to apologize for the slayings and offer his condolences, Pentagon spokesman George Little said.

Taliban spokesman Zabiullah Mujahid identified the killer as one of their sympathizers, Abdul Rahman. He said an accomplice inside the ministry helped Rahman get inside the compound to kill the Americans in retaliation for the Quran burnings.

That claim could not be independently verified, and it remained unclear whether the killer, who remained at large, was an Afghan security officer or someone simply wearing an Afghan uniform.

Little, the Pentagon spokesman, said Wardak indicated President Hamid Karzai was assembling religious leaders and other senior Afghan officials to take urgent steps to protect coalition forces.

Although Allen’s announcement will have the most direct impact on those managing Afghan military policy from Kabul, the relationship between Afghan and U.S. troops who live and fight alongside one another far from the capital also turned icy last week. On shared bases in eastern Afghanistan, U.S. military commanders ordered their troops to keep their distance from the Afghan counterparts until tension dissipated.

“The mission requires us to spend time with our Afghan counterparts, and lately we haven’t been able to do that,” said one military official in the east who spoke on condition of anonymity.

The killings Saturday were only the latest chapter in the deteriorating relations between the Afghans and the U.S.-led NATO coalition. Among the recent events that have heightened tensions are an Afghan soldier’s killing of French troops that led the French to move up their withdrawal date, and outrage over a video that showed four U.S. Marines urinating on bodies that were said to be those of Taliban fighters.

The Quran burning, however, took the animosity to a new level. On Thursday, two U.S. soldiers were shot to death by a member of the Afghan Army at a base in eastern Afghanistan, as protests about the Quran burning raged outside.

At least 28 people have been killed and hundreds wounded since Tuesday, when it emerged that Qurans and other religious materials had been thrown into a fire pit used to burn garbage at Bagram Air Field, north of Kabul.

A U.S. official said the unrest and shootings of U.S. personnel by their Afghan counterparts would make it much harder for both sides to agree in the coming weeks on the specific terms and timetable of NATO’s planned withdrawal from Afghanistan by the end of 2014.

NATO leaders are scheduled to meet in May in Chicago, where they had hoped to finalize details of the withdrawal from Afghanistan and the gradual handover of security responsibilities to Afghan forces, and report on progress regarding fledgling negotiations with the Taliban.

Compiled from The Associated Press, The New York Times and The Washington Post.

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