The Pentagon used an evangelical aid organisation as a front for a spying operation in North Korea, according to a US-based news website.

An investigation by The Intercept found evidence that the Humanitarian International Services Group charity (HISG), set up by Colorado-based Kay Hiramine, received funding from the Pentagon connected to espionage in the secretive state.

According to The Intercept, the scheme dated back to 2004 and was the brainchild of Lt Gen William 'Jerry' Boykin, himself an evangelical Christian. Hiramine's organisation had previously been a small-scale charity responsible for shipping medical supplies and disaster relief material to emergencies around the world. However, after it was taken up by military it received millions of dollars for its work which came ultimately from the Pentagon.

On one occasion a shipment of winter clothing to North Korea was used to conceal Bibles, whose importation was forbidden.

"We sent the Bibles in as a test run," a former senior Pentagon official told The Intercept. "They got through without the North Koreans discovering them."

Hiramine was tasked with finding transportation routes to move equipment and potentially clandestine operatives inside North Korea. According to another former military official, the Pentagon would eventually move sensors and small radio beacons through Hiramine's transportation network.

"We needed collection devices, spoofers" — used to disrupt North Korean military devices or radio signals — "and [equipment] to measure nuclear anomalies," the same former military official told The Intercept. The military hardware also included shortwave radios that could be used to help a downed pilot to escape in the event of a future conflict with North Korea.

Most of those who worked for HISG never knew about its links to the Pentagon, The Intercept report said.

The programme was eventually shut down in 2012 by now-retired Admiral William McRaven, who oversaw the Osama bin Laden raid.

"McRaven told us he shut it down because he was nervous about the flap if it ever got out that the Pentagon had used a bunch of evangelicals and missionaries as spies," said one former military officer, adding that if the programme had produced better intelligence McRaven would have considered keeping it up and running.

HISG was closed in January 2013. Former HISG programme director Tom Jennings told The Intercept: "We got no warning. We had no jobs, no severance, and no explanation. All they said was 'we lost our funding.'"

The revelations have caused outrage among lawmakers and in the aid community.

Rep. Jan Schakowsky, who served on the House Intelligence Committee from 2007 until this year, said she was unaware of the programme. "If true, to use unwitting aid workers on behalf of an intelligence operation, people who genuinely do humanitarian work, to turn their efforts into intel collection is unacceptable," she said.

"Now we have people who have been hired to do some good work and become unwitting accomplices to an intelligence mission? They can face all kinds of retaliation. It is completely unacceptable."

While The Intercept's story comes with copious documentary and interview evidence, others have queried the extent and effectiveness of HISG's North Korea operation. NK News questioned David Austin, former North Korean programme director of Mercy Corps, who said: "None of my former NGO colleagues had ever heard of this group, nor of Kay Hiramine."

Austin said: "If the article is true, and missionaries or aid workers were used – against their own knowledge – for military purposes, then it goes without saying that the leadership of HISG lost its humanitarian and religious integrity by selling its services to the Pentagon," he said, "(meaning) the administration would have put at risk the lives of true humanitarians serving in places like the DPRK, Afghanistan and Pakistan."

The Intercept attempted to contact Hiramine for comment but received no response.