William Howard Hughes Jr, who had top secret clearance while in the Air Force, was arrested without incident last week during a passport fraud investigation, the Air Force Office of Special Investigations said in a statement.
It said Hughes, who changed his name to Barry O'Beirne, admitted his true name after being confronted with inconsistencies about his identity.
"Capt. Hughes claimed that in 1983 he was depressed about being in the Air Force so he left, created the fictitious identity of O'Beirne and has been living in California ever since," the statement said.
Hughes, now 66, deserted after a brief assignment in the Netherlands where he worked with NATO officers.
He was last seen in Albuquerque, New Mexico, withdrawing $28,500 from his bank account at 19 different locations.
A spokeswoman for the Air Force Office of Special Investigations told the Albuquerque Journal that there was no indication that Hughes had any classified information or had shared any at the time of his disappearance.
"Until we have the whole story, we don't have the story," she added.
Hughes is being held at Travis Air Force Base in California and has been charged with desertion, a crime that carries up to five years' confinement.
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