Robert Hale, the comptroller of the Defense Department, said at a news conference that the losses were due to lost productivity during the 16-day shutdown which furloughed more than 400,000 Defense Department civilian employees at its height, Xinhua reported.
The Defense Department then managed to bring most of the furloughed employees back to work Oct 7 while the rest, about 5,000, came back to work Thursday.
The shutdown also generated a number of other costs that have yet to be calculated, Hale added.
The government shutdown was over, but it would take a while for the effects to fade, said Defense Secretary Chuck Hagel.
Hagel noted that Congress did not remove the shadow of uncertainty cast over the department.
"If this fiscal uncertainty continues, it will have an impact on our economy, our national security, and America's standing in the world," he added.
The government shutdown and the country's debt limit problem could make American allies nervous as well, the secretary added.
"Our allies are asking questions: Can we rely on our partnership with America? Will America fulfill its commitments and its promises?" he said. "These are huge issues for all of us, and they do impact our national security and our relationships and our standing in the world."