The Pentagon is ordering most of its approximately 400,000 civilian Defense Department employees back to work after being furloughed following the government shutdown.

The decision by Defense Secretary Chuck Hagel is based on the legal review of Pay Our Military Act, which was signed into law on September 30, 2013 - just hours before the government officially shut down.

"I expect us to be able to significantly reduce - but not eliminate - civilian furloughs under this process," Hagel said.

"Employees can expect to hear more information from their managers starting this weekend."

There has been much speculation from senior figures in the army and intelligence agencies that the shutdown is posing a significant threat to US national security.

“I’ve never seen anything like this. In my view I think this, on top of the sequestration cuts, seriously damages the safety and security of the nation,” James Clapper, the director of national intelligence, said during a Wednesday Senate Judiciary Committee hearing which was convened to discuss NSA surveillance powers.

“This affects our global capability to support the military, to support diplomacy, and to support our policymakers. And the danger here, of course, that this will accumulate over time - the damage will be insidious. So each day that goes by, the jeopardy increases," said Clapper.

The army is currently furloughing all “non-essential” personnel, particularly those not involved in live operations abroad.

Hagel said while on an official visit to south Asia this week that lawyers for the Pentagon and the US administration were looking at ways to expand the number of defense department personnel who are exempt from furloughs.

He also voiced concern that the shutdown damages America’s reputation among its allies as a reliable partner.

“It does cast a very significant pall over America’s credibility to our allies when this kind of thing happens,” Hagel told reporters traveling with him.

For many Pentagon workers, the shutdown is the second time this year that they have been forced to take unpaid leave. Back in August, over 600,000 civilian defense employees were required to take unpaid leave in an effort to reduce spending after across-the-board budget cuts went into force in March.

“This has been a very disruptive year for our people,” Hagel said.

Meanwhile, US sailors have complained about delays in annual payments of re-enlistment bonuses, which are typically paid by October 1. Military academies have reduced their scheduled classes and even commissaries that sell groceries to military families have been closed.

Earlier Saturday, the Republican-dominated House of Representatives unanimously voted to approve a bill which will see the 800,000 furloughed workers paid retrospectively once the crisis has been resolved.

The House voted 407-0 and the bill will now be sent to the Senate, which is controlled by the Democrats. The White House has announced that President Obama will sign the measure into law once it passes Congress.

The shutdown was the result of a lack of agreement between Republicans and Democrats in the House of Representatives over the passing of the federal budget.

The Republican majority in the House refused to accept President Obama’s Affordable Care Act, known as Obamacare, which formally went into effect on Tuesday.

On Saturday, Obama urged the House to “stop this farce” and end the shutdown by unconditionally approving the federal budget.