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."
Ron Burgundy interviews Peyton Manning on SportsCenter
Texas principal bans speaking Spanish, stirs controversy