By Warren P. Strobel,Ellen Nakashima and Katie Mettler Washington Post

The former senior CIA official found with more than $40 million worth of gold bars in his house allegedly created a fake, highly classified intelligence program that he used as a conduit to funnel millions of dollars for his personal use, according to people familiar with the criminal investigation.

David J. Rush, who was arrested last month and charged with one count of theft of public money, constructed what is known as a “special access program,” a sort of black box for the most secret intelligence operations, the people familiar with the investigation said. Even intelligence personnel with the highest security clearance cannot access an individual SAP, as they are known, without specific authorization.

The people, who spoke on the condition of anonymity to describe an ongoing investigation, said the criminal probe found that Rush “read in,” or initiated, two colleagues into the highly secretive sham program, effectively cultivating them as perhaps unwitting accomplices and preventing them from talking to others about it. He persuaded one of them to transfer millions of dollars to the program via a government contract that was also fraudulent, they said.

“He made up a contract,” one of the people said.

Rush, who worked in the CIA’s Directorate of Science and Technology, has not pleaded to the charges against him. At a detention hearing in federal court in Alexandria, Virginia, on Friday, a judge ruled that Rush posed a significant flight risk and ordered him to remain detained at the local jail pending trial.

The CIA, meanwhile, has put several agency officials on leave as FBI and spy agency investigations continue, two people familiar with the matter said. NBC News first reported that development. The people familiar did not disclose those officials’ names or positions. The science and technology directorate is the arm of the agency that creates technical espionage tools to aid U.S. spies and their agents abroad.

The account of those familiar with the criminal probe appears to raise serious questions about secrecy guardrails and vetting at the CIA.

It remains unclear, for example, how Rush could single-handedly create a “black box” for a fictional spy program without sign-off from his superiors. It is also unclear whether the two colleagues Rush brought into the fake program knew it was fraudulent.

One of the people familiar with the probe said Rush’s fake program involved “continuity of government” operations, or programs to keep the U.S. federal government running in the event of nuclear war, natural disasters or other catastrophes.

Rush apparently used the fake government continuity program and the contract to persuade a government defense contractor to purchase large amounts of gold, this person said.

Even more astounding, according to former U.S. officials and others familiar with the issue, is that Rush’s duties at the CIA included involvement in one of the government’s most sensitive intelligence-gathering programs, a project so secret that only a handful of U.S. intelligence officials and lawmakers knew of its existence, according to four people familiar with the matter.

Details of that program – separate from the fake project Rush allegedly created – remain highly classified. The Washington Post is withholding details about the program after U.S. officials warned that disclosure could jeopardize ongoing intelligence-gathering operations.

Rush was arrested following a May 18 FBI raid on his house, where agents seized 303 gold bars worth roughly $40 million, $2 million in cash and 35 luxury watches, according to a government affidavit.

The bulk of Friday’s detention hearing in federal district court was sealed to the public. For about 40 minutes, attorneys privately debated facts of the case that required top-secret security clearance, according to court documents.

In the hearing’s public portion, Assistant U.S. Attorney Gavin Tisdale told U.S. Magistrate Judge William Fitzpatrick that Rush was a “master manipulator” who “lied to colleagues” about basic facts of his pedigree and “lied to neighbors” about working as a Navy pilot.

“Mr. Rush simply cannot be trusted to abide by this court’s conditions,” Tisdale said, arguing he is a “serious flight risk” who is “fully able and willing to skirt the rules.”

Fitzpatrick ordered Rush to remain in detention, saying he had the skills, “means and motive” to flee.

Jessica Carmichael, Rush’s defense attorney, said during the court hearing she believed that Rush should be assigned an ankle monitor and allowed to await trial at home with his wife and children. She told the judge she had concerns that Rush was being held on the basis of “sensational allegations” from the government – some of which she had learned that morning – that are not related to the single criminal charge he currently faces.

In return, Tisdale said the case has been rapidly evolving since the original criminal complaint two weeks ago, which included just a “fraction” of the evidence investigators have now gathered. Rush, Tisdale said, is in a “world of trouble.”

Carmichael declined to comment after the court hearing.

So far there is no evidence that Rush was being paid by a foreign power for espionage, said one person familiar with the matter.

But the revelations raise significant questions about how the CIA and other government agencies allowed Rush to ascend to such a significant post, while failing to uncover his alleged misrepresentations about his educational history and military service.

“This is just staggering,” said Rep. Jim Hime of Connecticut, the top Democrat on the House Intelligence Committee. “Keeping gold bars and wads of cash in your house is not exactly top-notch tradecraft. From an oversight standpoint, how the hell did this happen?”

The government affidavit, filed May 20 in U.S. District Court in Alexandria, alleges that Rush lied to the CIA about his college degrees and Navy record, and fraudulently obtained $77,000 in military leave pay despite having been discharged from the Navy in 2015.

Former U.S. intelligence officials said they were stunned that Rush’s alleged misrepresentations were not flagged in what are normally lengthy and rigorous background checks for would-be CIA employees.

One of the officials described how he was administered blood tests, psychological exams and polygraph tests, then was required to sign a stack of forms before being hired. Government security officials double-checked his college transcripts.

“It’s shocking that he got by a process that scrutinizes everything,” said Marc Polymeropoulos, a former CIA operations officer whose field assignments spanned the globe. ‘’They interview friends, relatives, professors. It’s a full-on colonoscopy.’’

In addition to the CIA personnel actions, a senior employee at a U.S. defense contractor was fired, one person familiar with the matter said.

The May 20 government affidavit indicates that Rush joined the CIA around 2009, well before current Director John Ratcliffe took over.

Trump administration officials have briefed the House and Senate intelligence committees on the Rush case.

Rush had at least a temporary association with Deputy Secretary of Defense Stephen Feinberg, according to three current U.S. officials and one former official. It is unclear how the two men met. Feinberg served as chairman of the President’s Intelligence Advisory Board, which provides independent advice on U.S. spy programs, during President Donald Trump’s first term. NBC News first reported Rush’s ties to Feinberg.

Chief Pentagon spokesman Sean Parnell said that insinuations of a close professional relationship between the two men “are completely false and embellished. Deputy Secretary Feinberg never supported Mr. Rush’s career at any point in his life, nor did he endorse Mr. Rush for any career position.”

The government affidavit says that Rush claimed to have a bachelor’s degree from Clemson University and a master’s from Rensselaer Polytechnic Institute. An FBI investigation found no record of Rush ever attending either institution, nor any evidence to support his claim that he had been a Navy pilot.

Several of the people familiar with the case said the very government secrecy designed to protect valuable intelligence can be used to hide misconduct.

One of the people, a former top U.S. intelligence official, said that U.S. spy agencies often use “financial tradecraft” to move large amounts of money for intelligence operations without attracting the attention of adversary spy services from China, Russia and elsewhere.

It’s important, the former official said, that those countries don’t know the source or destination of the money. “The problem … it means that neither do we.”

Aaron Schaffer contributed to this report.