Hughes was single and stationed at Kirtland Air Force Base in Albuquerque, New Mexico, when he disappeared in July 1983, the Air Force said.
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.
Hughes told authorities he was depressed about being in the Air Force and made a decision to leave.
"Intelligence officers believe that Hughes was either captured by Soviet agents or voluntarily defected to the Soviet Union", the Times said.
At the time, Hughes was single and assigned to an Air Force center in New Mexico, where he had responsibilities including "classified planning and analysis of the North Atlantic Treaty Organisation command, control, and communications surveillance systems", the Air Force said. The interview was held with "Barry O'Beirne", but it didn't take long for officials to realize the man's true identity.
Hughes was supposed to travel to the Netherlands in July 1983 to work with North Atlantic Treaty Organisation officers on the operations of AWACS electronic surveillance planes. He was expected to return to duty at Kirtland on August 1, 1983. The only clue Hughes left behind was a trail of bank withdrawals, where he pulled out $28,500 from 19 different branches.
Before he mysteriously disappeared and landed on the Air Force Most Wanted list, Capt. William Howard Hughes Jr. phoned home to tell his mother and father that he was going to the Netherlands. Others speculated that he had defected -possibly to the Soviets - with the highly classified information, a notion that fomented conspiracy theories for years.
Hughes "was the "lead analyst" of the Command Control and Communication Surveillance Systems at the Air Force Operational Test and Evaluation Center at Kirtland Air Force Base in Albuquerque, N.M., which tests new space-related weapons systems", the Times said. One such anonymous official said, "He is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them".
An Office of Special Investigations spokeswoman told the Albuquerque Journal that there's no indication Hughes was involved with the Soviet Union or that any classified information was leaked.
"Until we have the whole story", she said, "we don't have the story".
Card said Hughes' family has been notified of his apprehension, but it is unknown whether they had been in contact with him or knew his whereabouts.
Hughes, now 66, was arrested by the Air Force Office of Special Investigations the next day.