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.
"On June 5, during a passport fraud investigation, the US Department of State's Diplomatic Security Service interviewed an individual claiming to be Barry O'Beirne", the Air Force said in a statement.
Air Force Capt. William Howard Hughes Jr. started at Kirtland in 1981, working on NATO's command, control and communications surveillance systems.
Hughes, a captain at Kirtland Air Force Base, was 33 when he vanished.
Hughes was unmarried when he disappeared, but the Seattle native had three sisters.
Hughes apparently lived in California under the assumed identity of Barry O'Beirne.
Hughes has claimed that he was depressed about his time in the Air Force and so made a decision to leave.
A former Air Force officer, Howard Hughes Jr., was missing for over 35 years. Hughes, now 66, was last seen after returning from a two week vacation in Europe and withdrawing more than $28.5K from 19 different locations in Albuquerque.
Hughes, who had top-secret clearance when he was in the Air Force, worked on classified North Atlantic Treaty Organisation systems, the AFOSI says.
He had just completed a stint in the Netherlands, where he worked with North Atlantic Treaty Organisation officers on the Airborne Warning and Control electronic surveillance aircraft. On Aug. 1, 1983, he was supposed to return to work at Kirkland, but never turned up.
There was even speculation that Hughes may have been abducted by or defected to the Soviets.
Hughes is charged with desertion and awaiting pretrial confinement at Travis Air Force Base in Fairfield, Calif.
Hughes reportedly returned to New Mexico on leave in July 1983.
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.
A couple years later, in July 1986, the Los Angeles Times reported that, after several French and American rocket ships exploded following improper launches, intelligence officers believed the rockets may have been sabotaged with help from Hughes.
Mr Szulc also said an intelligence officer told him Capt Hughes was "worth his weight in gold to the Russians in terms of future "Star Wars".
An Office of Special Investigations (AFOSI) spokeswoman told the Albuquerque Journal that there's no indication Hughes was involved with the Soviet Union or that any classified information was leaked.
Hughes faces desertion charges, which carries a maximum of five years in prison.
"Until we have the whole story, we don't have the story", Ms Card said. Hughes was recently apprehended 35 years after he is alleged to have deserted.