US President Barack Obama signed a last-minute deal early Thursday to end the partial government shutdown and raise the debt ceiling.

Obama signed the bill into law without further comment after both the House and Senate approved it late Wednesday.

Speaking shortly after the Senate vote, the president said he would sign the bill as soon as it came to his desk and the process of reopening government would begin "immediately."

He thanked leaders from both the Democrats and the Republicans for working out an agreement to end the government shutdown and raise the debt ceiling.

"Hopefully next time it won't be in the 11th hour," he said. "We've got to get out of the habit of governing by crisis."

Minutes after Obama signed the bill, White House budget director Sylvia Mathews Burwell issued a directive to employees, saying the government would try and make the transition back to fully operational as smooth as possible.

"All employees who were on furlough due to the absence of appropriations may now return to work. You should reopen offices in a prompt and orderly manner," she said.

"This has been a particularly challenging time for Federal employees and I want to thank our Nation's dedicated civil servants for their continued commitment to serving the American people," Burwell added.

The bill ended weeks of tension and stalemate between the two parties, which lurched the federal government into the first partial shutdown in 17 years and pushed the country to the brink of an historic default.

Congress defused the risk just one day before the deadline set by the US Treasury Department, which said it would exhaust the "extraordinary measures" it had taken to keep paying bills on Oct. 17, with merely 30 billion US dollars cash on hand.

The short-term bill provides a temporary fix for the country's fiscal issues, but will not resolve the fundamental divide between the Democrats and the Republicans over Obamacare, which caused the standoff between the two parties.

The deal also raises the possibility of another battle early next year when the government runs out of funds and the Treasury's borrowing authority ends again.