Responding to Hughes' claims of deserting the air-force cause he was depressed, AFOSI spokeswoman Linda Card said there were many more questions to be answered as the investigation continues.
He had been sent to the Netherlands July 18, 1983, to work with North Atlantic Treaty Organisation officers and was due back in Albuquerque on August 1, the Air Force said.
A U.S. Air Force officer with top-secret clearance was reportedly found 35 years after he was declared missing.
He has been living in California under a fake identity ever since his defection.
Hughes told authorities after his capture on Wednesday that he was depressed about being in the Air Force and chose to leave.
OSI agents assigned to Travis AFB in northern California went to his home and arrested the fugitive captain without incident. The only clue Hughes left behind was a trail of bank withdrawals, where he pulled out $28,500 from 19 different branches.
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.
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He had just returned from a temporary assignment in The Netherlands, where he worked with North Atlantic Treaty Organisation officers on the Airborne Warning and Control electronic surveillance aircraft.
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.
Hughes' sister, Christine Hughes, told the Associated Press in a January 1984 article that the family believed he had been abducted, according to the Albuquerque Journal.
After several rocket ship failures in the U.S. and France, including the Challenger space shuttle disaster in 1986, Los Angeles Times journalist Tad Szulc theorised Capt Hughes may have been to blame.
Hughes is charged with desertion and awaiting pretrial confinement at Travis Air Force Base in Fairfield, Calif.
"He is worth his weight in gold to the Russians in terms of future 'Star Wars, ' if we have them", the LA Times quoted an intelligence officer as saying.
In the years after Hughes went missing, a slew of NASA catastrophes, such as the space shuttle Challenger disaster of 1986, as well as the explosion of the Ariane rocket in French Guinea, caused national security commentators to speculate whether the disasters were related and possibly the result of Soviet sabotage. If convicted, he might face maximum penalties of dishonorable discharge, forfeiture of all pay and confinement of five years.
"Until we have the whole story, we don't have the story", Card said.