US Defence Secretary Chuck Hagel said the decision to recall the Pentagon employees was based on an interpretation of the Pay Our Military Act.
A budget row over President Barack Obama's showpiece 'Obamacare' healthcare reform law between Republicans and Democrats has forced the closure of federal services since Tuesday.
But both sides have now voted to approve back-pay for the 800,000 federal workers sent home without salaries.
In a rare moment of bipartisan co-operation, the House of Representatives yesterday approved by 407-0 a bill to pay the federal workers once the shutdown ends.
But there is still no sign of any deal on the federal budget or any measure to raise the nation's USD 16.7 trillion debt ceiling.
Neither the House nor the Senate plans to meet again until tomorrow afternoon, meaning the shutdown will have lasted at least seven days.
The shutdown has left federal employees on unpaid leave and closed national parks, tourist sites, official websites, office buildings, and more establishments.
Congress must act by October 17 in order to avoid a debt default by the US government. The government will run out of cash on that day for the first time in US history unless its debt ceiling is raised.
Republicans who control the House of Representatives have refused to approve the budget, saying they would only do so if the healthcare programme was delayed or stripped of funding.
Obama and the Democrats have refused, noting the law was passed in 2010, subsequently approved by the Supreme Court, and was a central issue in the 2012 election which Obama won.
Obama cancelled his Asia visit because of the shutdown.
In his weekly radio address, the President urged the Republicans to "end this farce".
"For as reckless as a government shutdown is, an economic shutdown that comes with default would be dramatically worse," he said.
The President has refused to negotiate with the Republicans until they pass a temporary bill to end the shutdown and raise the debt limit.