When investigators confronted him about "inconsistencies about his identity", the man confessed that his real name was William Howard Hughes Jr., and that he deserted the Air Force in 1983, according to the Office of Special Investigations.
Air Force Capt. William Howard Hughes Jr., shown in a decades-old official Air Force photo, had been living under the name Barry O'Beirne, the service said. This is the last time he was seen as William Howard Hughes until last week. He was working at the Air Force Operational Test and Evaluation Center at the Kirtland Air Force Base in New Mexico. Hughes, a Seattle native was arrested without incident on Wednesday.
A U.S. Air Force officer with top-secret clearance was reportedly found 35 years after he was declared missing. He had been living in California ever since, he said.
After his arrest, Hughes told investigators that he was depressed about being in the Air Force and made a decision to leave.
At the time of his disappearance, the Air Force said Hughes had a "Top Secret/Single Scope Background Investigation" clearance.
Instead, investigators said Capt. Hughes went to 19 Albuquerque bank branches and withdrew a total of $28,500 from his account.
It was July 17, 1983, and the Air Force was sending Hughes overseas on a mission to help North Atlantic Treaty Organisation test aircraft surveillance systems. On Aug. 1, 1983, he was supposed to return to work at Kirkland, but never turned up. "We do not feel he disappeared voluntarily", his sister, Christine Hughes, said.
Capt Hughes is now being held at Travis Air Force Base in California, a statement from the USAF's office of special investigations said. Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
However, Linda Card, a spokeswoman for the air force office of special investigations, told the Albuquerque Journal that investigators now see "no indication that he had any classified information or that he gave any classified information".
In the wake of those disasters, Los Angeles Times journalist Tad Szulc reported in July of 1986 that intelligence officers believed the rockets may have been sabotaged with Hughes' help.
"He is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them", Szulc quotes an unidentified intelligence officer as telling him.
"They (AFOSI investigators) said at this point there's no indication that he had any classified information or that he gave any classified information..."
Last year, there was uproar when Bowe Berhdahl was spared prison time after being found guilty of deserting his Afghan outpost - instead he was reduced to private in rank, dishonourably discharged and lost pay.
"Until we have the whole story, we don't have the story", Card said.