A C.I.A. employee who was found recently with $40 million of gold bars in his house had created a secret intelligence program to funnel millions of dollars from the federal government to himself, according to two U.S. officials.

David Rush, the employee, created a fake “special access program,” a sensitive intelligence tool that has highly limited visibility even within the C.I.A., the officials said.

Mr. Rush was arrested late last month and charged with theft of public funds based on a lie about joining the Navy Reserve after serving in that branch of the military, from which he was discharged in 2015, according to court documents. Prosecutors accused him of getting unwarranted pay by filling out time sheets based on the fraudulent claim of being a Navy reservist.

Mr. Rush, a C.I.A. officer for 17 years, was arrested on May 19 after F.B.I. agents found 303 gold bars weighing about one kilogram each in Mr. Rush’s home, according to an affidavit. The agents also seized nearly three dozen luxury watches, many of them Rolexes.

The U.S. officials who said that Mr. Rush had created a fake “special access program” did not provide details of the program, or explain how Mr. Rush used it to take government money. The Washington Post reported earlier on Mr. Rush’s use of the fake program.

Jessica Carmichael, a lawyer for Mr. Rush, declined to comment.

The F.B.I. and C.I.A. issued a joint statement last month following Mr. Rush’s arrest. “After a C.I.A. internal investigation identified potential violations of the law, C.I.A. director John Ratcliffe referred the information to the F.B.I. for a law enforcement investigation,” the agencies said.

From last November to March, Mr. Rush asked for, and received, “a significant quantity of foreign currency and tens of millions of dollars in gold bars for work-related expenses,” court documents said.

When the C.I.A. conducted a review of where the gold and currency were stashed, the agency was “unable to locate the gold bars or significant amounts of the foreign currency,” the documents said. Mr. Rush also had $2 million in U.S. currency in his home.

Mr. Rush’s case has raised questions about the C.I.A.’s employee vetting process, and the agency’s oversight of sensitive intelligence work. Some lawmakers have demanded detailed answers and accountability from the agency.

Mr. Rush is being detained in Alexandria, Va. On Friday, following a hearing, Judge William E. Fitzpatrick of the U.S. District Court for the Eastern District of Virginia ruled that Mr. Rush had to remain in detention, since he was a flight risk.

Mr. Rush also has a history of lying to the C.I.A. about his college education, according to court documents.