The government's reopening and extension of the borrowing authority came after the Senate and the House voted to reopen the government through Jan. 15, suspend the debt ceiling through Feb. 7 and lay the groundwork for talks over broader budget issues.
Hagel said while that means the Pentagon can return to critical national security issues, the short-term resolution limits his ability to look beyond the immediate fiscal horizon.
More than 400,000 civilian employees at the Defense Department were furloughed by a partial government shutdown that began Oct. 1. All but 5,000 returned to work under a special provision Oct. 7 and remaining employees returned to work after lawmakers passed the short-term deal this week.
Although lawmakers can get to work on negotiating a long-term spending measure, Hagel said it was a legacy of political uncertainty that was troubling him.
"Our allies are asking questions: Can we rely on our partnership with America? Will America fulfill its commitments and its promises?" he said at a Thursday press conference. "These are huge issues for all of us, and they do impact our national security and our relationships and our standing in the world."