According to a news release, Hughes admitted his identity during an interview with the U.S. Department of State's Diplomatic Security Service as part of a passport fraud investigation.
While working at his permanent duty station at Kirtland AFB, New Mexico, the Air Force assigned Hughes to a temporary duty station in the Netherlands in July 1983.
Interviews with Hughes' friends and associates and inquiries with law enforcement agencies in the U.S. and overseas failed to locate him, the statement said, and he was formally declared a deserter on December 9, 1983. Hughes created a fake identity and lived under the pseudonym "Barry O'Beirne" for over three decades.
Former Air Force officer William Howard Hughes, Jr., (seen in a current mugshot) was arrested this week.
Instead, investigators said Capt. Hughes went to 19 Albuquerque bank branches and withdrew a total of $28,500 from his account.
At the time of his disappearance he had just returned from the Netherlands, where he had been working with North Atlantic Treaty Organisation officers.
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He told his parents he was supposed to come back from the Netherlands on August 1.
But Card said no classified information leaks are suspected, nor is there an indication that Hughes was involved with the Soviet Union, but the investigation is ongoing.
It is unknown whether family had been in contact with Hughes or knew of his whereabouts following his 1983 disappearance.
His mysterious disappearance during the Cold War spurred theories that he had been abducted by the Soviet Union or defected to what was then known as the USSR to work against the US.
In Jan. 1984, Hughes' sister, Christine Hughes, told the Associated Press that the family believed Hughes had been abducted. If convicted, the officer could face reduction in rank, forfeiture of all pay and allowances, confinement in a military prison for up to five years and a dishonorable discharge, FindLaw.com reports.
In a 1986 Los Angeles Times commentary titled "Sabotaged Missile Launches?" for example, the former longtime New York Times foreign correspondent Tad Szulc wrote: "The French and American accidents are adding up to a freaky pattern, surrounded by unusual coincidences and unexplained events, deeply preoccupying Western intelligence".
"Szulc quoted an unidentified intelligence officer who told him, "[Hughes] is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them".
"Until we have the whole story, we don't have the story", Ms Card said.