Pentagon prepares shutdown instructions

Defense officials also say they are trying now to get clarity on what positions are essential and non-essential. Essential employees would still report to work during a shutdown.

DOD officials also are trying to determine what to do about positions directly supporting ongoing conflicts.

Air Force Secretary Michael Donley said Tuesday officials are trying to determine "what to do with the military and civilian workforce."

As the clock ticks toward a government shutdown, defense-minded lawmakers continued to express concerns about service members not getting paid, especially ones who are deployed in combat zones and have families back home depending on those funds.

The Defense Department has "been through this many times before, so we're not having to learn ... how to do this again,” Morrell said.

"We have fundamental understanding of this.  We can do this relatively quickly.  It's not without pain, but we are familiar with how to plan for this," he said.

Asked if service men and women would not get paid during a shutdown, Morrell replied: "We're not alone in that — that's something that is potentially facing all government employees."