It is the stuff of spy novels, but a new investigation published Monday reveals that the U.S. Pentagon for years funneled millions to a charity organization employing it to serve as the front group for global espionage—very real revelations that experts warn could have dangerous implications for aid workers worldwide.

After a months-long investigation, The Intercept's Matthew Cole, with help from Margot Williams and Lee Fang, exposes the reach of a highly-classified Department of Defense program, which ran from December 2004 to 2013.

The program was reportedly the "brainchild" of Lt. Gen. William "Jerry" Boykin, an evangelical Christian who served under President George W. Bush. After the 9/11 attacks, Boykin was charged with expanding the intelligence gathering arm of the DoD and, "taking a page from the CIA's playbook," began tapping NGOs to use as a cover for Pentagon espionage operations.

The exposé highlights one group, the Colorado Springs-based Christian organization Humanitarian International Services Group, or HISG, whose founder, Kay Hiramine, had for years been on the Pentagon payroll and whose organization reportedly had millions funneled to it via a "complex web" of private trusts and nonprofits.

The Pentagon reportedly employed HISG, which provided disaster relief and supplies to poor and war-torn countries, to infiltrate North Korea to gain access and information regarding its nuclear program—relying on the organization's "unwitting" employees, volunteers, and contacts to do so.

The Intercept reports:

The Pentagon tasked Hiramine with gathering the intelligence it needed inside North Korea, and Hiramine would in turn utilize HISG's access to the country to complete the assignments, according to two former military officials with knowledge of the effort. Hiramine, in his role as CEO of HISG, tapped Christian missionaries, aid workers, and Chinese smugglers to move equipment into and around North Korea — none of whom had any idea that they were part of a secret Pentagon operation. ... Because American intelligence has so few assets inside North Korea, much of Hiramine's task was to find transportation routes to move military equipment — and potentially clandestine operatives — in and around the country. The Pentagon would eventually move sensors and small radio beacons through Hiramine's transportation network, according to another former military official. Much of what Hiramine was doing was what the military refers to as "operational preparation of the environment," or OPE, a category that encompasses clandestine intelligence gathering and prepositioning equipment inside a country for future conflicts.

In one early "test run," an HISG shipment of charity clothing included a secret cache of Bibles in order to see if supplies could get into the country without being discovered.

As Cole notes, HISG "was one of several NGOs used by the Pentagon in this way. Some, like HISG, already existed as fledgling organizations, while others were created from scratch by the Pentagon."

The investigation's findings, "that the Pentagon used an NGO and unwitting humanitarian volunteers for intelligence gathering," constitutes a major transgression and threatens the safety and work of aid organizations worldwide.

Sam Worthington, president of InterAction, an association of nearly 200 American NGOs, told the reporters that such activity "violates international principles" and places legitimate aid and development workers at great risk.

"It is unacceptable that the Pentagon or any other U.S. agency use nonprofits for intelligence gathering," Worthington said. "It is a violation of the basic trust between the U.S. government and its civic sector."

Indeed, a CIA-directed mission in 2011 which employed a Pakistani doctor to gather DNA samples of Osama bin Laden's presumed family members, under the guise of a hepatitis vaccination program, has resulted in numerous attacks on "legitimate" medical groups.

Further, as noted by Sarah Knuckey, Columbia Law professor and director of the school's Human Rights Clinic, these findings also give "rhetorical ammo" to repressive governments seeking to restrict NGO activities within their borders.

HISG was reportedly shuttered in 2013 after Adm. William McRaven shut down the North Korean spying operation the year before. It's "unclear" if President Obama was ever briefed on the program, The Intercept notes, and the White House declined to comment.

The Intercept investigation relied on interviews with more than a dozen current and former military and intelligence officials, humanitarian aid workers, missionaries, U.S. officials, as well as former HISG staffers. The Pentagon provided no comment on HISG or the espionage operations in North Korea.