Lieutenant General Ron Lewis left his post as senior military assistant after meeting Carter, a US defense official said on condition of anonymity, just weeks after Carter described Lewis as someone "to count on."
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"The secretary was very surprised to learn about the allegations" late Tuesday, the official said, without specifying the nature of the allegations.
In a statement, Carter said he had referred the matter to the Defense Department's Inspector General, which confirmed that an inquiry had been opened.
"Today, I made the decision to remove my Senior Military Assistant Lieutenant General Ron Lewis from his position after learning about allegations of misconduct," Carter said.
"I have confidence in the Inspector General's ability to determine the facts. The Department of the Army will then take action as appropriate."
Lewis, a former attack helicopter pilot, served in Iraq and Afghanistan.
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Carter publicly praised him just a month ago at an Army event in Washington, saying: "Time after time, whenever I've needed Ron's counsel and vision, I've been able to count on him."
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