Ex-CIA officer David Rush’s alleged years-long scheme that netted him $40 million in gold bars and a top-secret security clearance has those in the Clandestine Service community questioning how he slipped through the fastidious vetting process — and who else may be flying under the radar.

Former CIA staff operations officer Tracy Walder was baffled over the stunning allegations against Rush and believes they could point to a much more troubling issue within the agency.

“This would have been a large-scale lying cover-up. There would have had to be a lot of other co-conspirators,” Walder told The Post.

“They are going to go back at least 10 years in terms of people you know, people you are friends with. He would have had to ask all those people to lie for him. Or did he lie to them?”

The FBI raided Rush’s Virginia home May 18 as part of an investigation into whether he lied about his military and academic background, and found 303 1-kilogram gold bars worth over $40 million, $2 million in US currency and 35 luxury watches, “many of which” were Rolexes.

According to an affidavit, Rush obtained the gold bars by making a series of requests between last November and March of this year, claiming he needed the bullion for “work-related expenses.”

Walder surmised Rush may have forged documents, or maybe “it’s a lazy or incompetent background investigator” who missed the red flags across his three separate applications to the agency before he was finally hired in 2009.

“On a personal level, I was frustrated because obviously I went through the whole security clearance process and it’s not fun. How in the world did this slip through the cracks?” she wondered.

“The fact that this slipped through the cracks makes me concerned that there are other people who slipped through the cracks.”

Walden said CIA candidates must endure a lengthy, invasive vetting process in order to get hired.

“They don’t just verify your college. They came to my sorority house. They talked to my sorority sisters. They came to my parents’ house. They went to the friends of the friends of my parents,” she said.

As for the king’s ransom in gold bars Rush accumulated, she said sometimes the agency receives requests for currency or gold, but never without accounting for every penny.

“It’s not unusual to need money to meet with assets overseas. You have to have a way to pay them and you don’t just run a credit card. They’re essentially committing treason, so you’re going to pay them in whatever currency they want,” she said.

“But I cannot think of an asset that needs $40 million in gold bars,” she added.

“There is a whole process that we go through to get that money. I don’t just walk into the logistics office and say, ‘Excuse me, I need $100,000 tomorrow.’ There is a form I have to fill out. It’s not a bank vault you walk into. It doesn’t work like that.”

She said even if Rush lied and said his asset was someone ultra-high-profile like Russian President Vladimir Putin, “the CIA would know who has what asset and who is working with what asset and if they are real or not.”

But she said even if an agent asks for $10, “you still have to fill out that form and be accountable for it. It’s not a free-for-all.”

She said even after the pre-hiring vetting, CIA employees are subject to rigorous scrutiny of their credit and finances.

Walder said when she was just getting started in her career and money was tight and she was living in a rough neighborhood, her parents helped her out with $75 a month to park her car in a garage. Eventually, the agency flagged even that pittance.

“It’s annoying … I remember being flagged about that,” she said, recalling the agency peppered her with questions about the money: “Where did you get this? Why did you get it? What was it for?”

She eventually had to give them her parents’ banking information to prove where the $75 was coming from.

Walder hypothesized that maybe “they let this happen on purpose to see who he was talking to and what he was doing,” but dismissed her own theory due to the “spectacle” of the FBI raid on his home.

“It doesn’t make sense,” she said.

Rush, until recently a “senior executive service-level employee” at the CIA, is facing charges of theft of public money. He is being held in custody.

His attorney declined to comment.