But federal authorities were interviewing a man named Barry O'Beirne last Tuesday as part of a passport fraud investigation, and when they challenged him over his identity's inconsistencies, he said he was Hughes and had deserted the Air Force in 1983, the news release said.
Hughes was unmarried when he disappeared, but the Seattle native had three sisters.
The report notes that Hughes was officially declared a deserter on December 9, 1983 after he returned from duty in Europe.
Hughes was assigned to the Air Force Operational Test and Evaluation Center, where he was involved in classified planning and analysis of the North Atlantic Treaty Organisation command, control, and communications surveillance systems. 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.
Air Force Capt. William Howard Hughes Jr. started at Kirtland in 1981, working on NATO's command, control and communications surveillance systems.
William Howard Hughes Jr. vanished in 1983 after returning from duty in Europe and withdrawing almost $30,000 from his bank account.
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 supposed to return to Albuquerque, N.M., on August 1 of that year.
TaskandPurpose reported Hughes' auto being found at the Albuquerque airport and a search of his home in the 1900 block of Chandelle Loop NE revealed notes of planned activities and books to read upon his return.
That officer, Capt. William Howard Hughes Jr., was apprehended in California on Wednesday, more than 30 years after his mysterious disappearance.
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. There were even rumors he might have been defected to the Soviet Union.
Hughes, now 66, was taken into custody reportedly told investigators that he was "depressed" in the service and created a fake identity to start a new life.
Hughes apparently lived in California under the assumed identity of Barry O'Beirne.
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.
It is unknown whether family had been in contact with Hughes or knew of his whereabouts following his 1983 disappearance.
Hughes also had top security clearance and deserted his post on July 25, 1983.
He is awaiting pre-trial confinement. 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.