The Pentagon says the 16 day partial government shutdown cost the DOD more than $600 million.
Department of Defense Comptroller, Robert Hale, says he expects the cost to go up.
Aside from the monetary cost, DOD officials say the shutdown and civilian furloughs took hits to morale and confidence.
Defense Secretary, Chuck Hagel, says the lack of certainty on funding is tiring for everyone at the DOD.
He said, "People have to have some confidence that they have a job they can rely on."
He went on to say, "We can't continue to do this to our people".