WASHINGTON — The Defense Department specializes in mobilizing for massive operations on short notice. But officials at the Pentagon are finding this week that preparing to shut down much of the government’s largest bureaucracy by midnight Monday is proving messier than many challenges.

At the military’s Arlington, Va., headquarters and on bases around the world, supervisors have been cloistering one-on-one with 3 million active-duty military, civilians and reservists to tell them whether to report to work Tuesday morning. The payroll staff has scrambled to figure out how Pentagon computers would cut paychecks if much of the staff was told to stay home. On Friday, assorted deputies, assistants and analysts were scurrying in and out of the offices of Defense Secretary Chuck Hagel and his comptroller, Robert Hale, for last-minute briefings and conference calls with veterans and commanders around the world.

“The planning itself is disruptive,” an exhausted Hale told reporters. “People are worrying right now about whether their paychecks are going to be delayed, rather than focusing fully on their mission.”

Shutdown planning has eaten up “probably thousands of hours in employee time better spent on supporting national security,” Hale said.

The tempo was similar at just about every federal agency this week, with managers racing from planning meetings to town hall gatherings with their employees.

Hundreds of thousands of employees who got word Friday that their jobs would not be essential prepared to turn in their government-issued BlackBerrys and iPhones on Tuesday morning, while colleagues who must still report to the office wondered how their agencies would carry out their missions.

In the Defense Department, about 400,000 civilians will have to stay home if Congress does not pass a bill to keep the government open, Hale said.

Preparing for even a partial closure is a unique challenge for the Defense Department, which has a global reach that includes about 200 schools, 250 commissaries, and 700 hospitals and clinics. The department’s mission is singular within the federal government. The Pentagon must continue to support its combat operations in Afghanistan and deployments in many corners of the world.

In his Office of Public Affairs on Friday, Army Col. Steve Warren was coming to grips with the reality facing his staff.

“I’ve got no essentials in here, and I’m concerned,” Warren said.

Warren was worrying about manning hundreds of Pentagon websites and Twitter and Facebook, which get information to the public.

“Guess who runs most of them?” he said. “Civilians who are not essential.

“There’s no simple answer to any of this,” Warren said.

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