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Mr. Hale said the law the defense secretary to determine who would be recalled, “which our lawyers concluded clearly implied that a blanket recall was not supported.”

He called on lawmakers to end the shutdown, saying that the lapse has forced the Pentagon to waste time and “a good deal of the public’s money.” The Pentagon will spend more than $600 million in retroactive pay to furloughed civilians for work they did not do, he said.

Christopher A. Preble, vice president for defense and foreign policy at the libertarian Cato Institute think tank, said retroactive pay not only will waste money but also will harm the morale of civilians and military personnel who have worked through the shutdown.

“It sends an unfortunate message to the people who were not furloughed and who also get paid, who actually had to work, and who actually have to work more because they are carrying the load for those furloughed,” Mr. Prebel said. “The manner in which [the shutdown has] been done can be just very disruptive.”