Roughly 350,000 Pentagon civilian employees were called back to work because of the Pay Our Military Act, which was signed shortly before last week's shutdown.
Defense Secretary Chuck Hagel revealed workers were ordered back to work based on an interpretation of the law. Federal attorneys argued that the law allowed the Pentagon to slash furloughs for "employees whose responsibilities contribute to the morale, well-being, capabilities and readiness of service members," according to The Associated Press.
The law ensures that members of the military who have remained at work throughout the shutdown receive pay on time while also allowing Pentagon civilian employees the same exemption.
The shutdown that began Tuesday left more than 800,000 federal workers on furlough and closed down museums and national parks temporarily.
House Republican leaders say the Affordable Care Act, the president's signature health care law, should be delayed or defunded before the House passes a bill to continue to fund the government. The president and Democrats in Congress, on the other hand, insist there should be no strings attached to the government funding measure.
It is being feared that the standoff over the shutdown would further intensify the fight expected over the debt-ceiling, which must be raised by Oct. 17 to avoid a potential default on the U.S. debt.
"They're not doing me a favor by paying for things that they have already approved for the government to do. That's part of their basic function of government; that's not doing me a favor. That's doing what the American people sent them here to do, carrying out their responsibilities," President Obama told NPR.
"I have said consistently that I'm always happy to talk to Republicans and Democrats about how we shape a budget that is investing in things like early childhood education, rebuilding our roads and bridges and putting people back to work, growing our economy, making sure that we have the research and development to stay at the cutting edge and that deals with some of our long-term debt issues.