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WASHINGTON — The shooting deaths of two U.S. military advisers in the Afghan capital and the quick decision to pull coalition personnel from all government ministries injected a sobering measure of doubt about the reliability of the most important U.S. ally in the war.

The Pentagon condemned what it called the murder of the two American officers but said it was committed to working closely with the Afghans to counter violent extremism and to stabilize the country.

President Barack Obama telephoned the top U.S. commander in Afghanistan, Gen. John Allen, with condolences. And the White House praised President Hamid Karzai’s efforts to restore calm in his country.

In a written statement, Defense Secretary Leon Panetta’s press secretary said Afghan Defense Minister Gen. Abdul Rahim Wardak called Panetta on Saturday to offer his condolences and to apologize.

“Secretary Panetta appreciated the call and urged the Afghan government to take decisive action to protect coalition forces and curtail the violence in Afghanistan after a challenging week in the country,” spokesman George Little said.

He said Wardak told Panetta that Karzai was assembling religious leaders, parliamentarians, Supreme Court justices and other senior officials “to take urgent steps” to stop the violence.

White House press secretary Jay Carney said the administration welcomes Karzai’s statements “encouraging peaceful expressions, and his call for dialogue.”

Even if Saturday’s killer turns out not to be an Afghan, the deaths compound a perception of insecurity in the heart of Kabul after a series of security failures and Afghan outrage over U.S. burning of Muslim holy books.

The Taliban claimed responsibility and said the attack was in retaliation for what U.S. officials have said was the inadvertent burning of Afghan religious materials, including copies of the Koran, at Bagram air base north of Kabul.

Allen, who commands U.S. and coalition forces in Afghanistan, said the killer’s actions “will not go unanswered.” Citing security reasons, he recalled all coalition personnel from Afghan ministries.

NATO forces have advisers embedded in many Afghan ministries, both as trainers and to help manage the transition to Afghan control as foreign forces prepare to withdraw by the end of 2014.

A White House statement said Obama thanked Allen for his steps to protect U.S. troops and to encourage calm. It said the U.S. remains committed to “a partnership with the government and people of Afghanistan.”

Still, the killings are likely to provide momentum for critics of President Barack Obama’s war policy, as well as Republicans who fault him for having apologized for the Koran burning.

Obama’s apology Thursday, shortly after Allen expressed deep regret, was seized on by the president’s Republican rivals as a sign of American weakness. Presidential primary candidate Newt Gingrich said it was the Afghans who should be apologizing.

These tensions coincide with planned administration meetings in Washington in the week ahead with the Afghan ministers of defense and the interior.

It was unclear Saturday whether the session, including one on Thursday with Panetta at the Pentagon, would go on as scheduled.

Those talks are seen as important in the lead-up to a NATO summit meeting in May in Chicago, when the alliance and Karzai intend to determine the path to turning over full security responsibility to the Afghan government by the end of 2014.

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