The force, said to be ten times the size of the CIA's clandestine element, is made up of operatives working undercover, with some of them embedded in top companies around the world, according to Newsweek.
Agents in the "signature reduction" programme, developed by the Pentagon over the past 10 years, are engaged in online as well as real life assignments and are often soldiers, civilians and contractors who evade detection with false identities.
Newsweek reports that the secret army is carrying out its duties without the knowledge or consent of Congress.
North Korea, Russia and Iran are believed to be just some of the counties seen as hostile to the US where the agents are working. The agency has a reported budget of $900 million.
One intelligence officer, who is unnamed, says the army operates in “signature reduction”, although the term is not officially recognised by the Department of Defense. It is, however, used to define "measures that are taken to protect operations".
Although some of the agents work in the shadows, Newsweek pointed to the case of Ryan Fogle as an example of when agents get caught.
Mr Fogle is an alleged CIA agent who was detained in Russia for allegedly trying to recruit a Russian intelligence officer.
Footage of Mr Fogle being berated by plain-clothes FSB interrogators was released to Russian television channels in May 2013, along with photographs and video footage of a bizarrely old-school array of spying tools, including two wigs, a compass, a map of Moscow and a stack of 500 Euro notes.
At the time, the state department confirmed one of its agents had been detained, but refused to be drawn on claims they were actively engaged in trying to recruit Russian operatives.
Newsweek's investigation also revealed how a company based in North Carolina trains agents how to change their age and appearance using disguises and equips them with a silicone sleeve that allows them to alter their fingerprints.
According to Newsweek, up to 30,000 of the country's signature reduction troops are operating around the world from Pakistan in the Middle East to West Africa in the south.
The Independent has contacted the state department for comment.
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