A missing US officer with top-secret clearance has been discovered living under another name some 35 years after mysteriously vanishing from his Air Force base.

Captain William Howard Hughes Jr was last seen withdrawing US$28,500 ($37,500) from several banks in New Mexico in July 1983, officials said.

Captain Hughes had just returned from a holiday in Europe and failed to report for duty in Albuquerque in August. He was declared a deserter four months later and his whereabouts remained a mystery until now.

The US Air Force Office of Special Investigations announced on Tuesday that Captain Hughes had been discovered earlier this month living in California.

“On June 6, 2018, Air Force Office of Special Investigations Detachment 303 Special Agents at Travis Air Force Base, California, apprehended Air Force fugitive Captain William Howard Hughes, at his California residence without incident,” the Air Force announced.

Captain Hughes had been living under the name Barry O’Beirne.

Investigators discovered Captain Hughes’ secret identity during a passport fraud investigation and confronted him about inconsistencies regarding his credentials.

Captain Hughes eventually admitted that his name was not O’Beirne.

Hughes said he was depressed about being in the Air Force. Photo: AFOSI

He told authorities after his capture that he was depressed about being in the Air Force and decided to leave. He said he had created a fake identity and lived in California since he vanished in 1983, according to the statement.

Captain Hughes was involved in classified planning and analysis of NATO’s control, command and communications surveillance systems during the Cold War. He specialised in radar surveillance.

He had a “top secret/single scope background investigation” clearance at the time of his disappearance, according to the statement.

Based at at Kirtland Air Force Base, Captain Hughes was 33 when he vanished, according news reports at the time of his disappearance.

“Captain Hughes, who was single, was dispatched to the Netherlands on July 18, 1983, to work with NATO officers on the operations of Airborne Warning and Control electronic surveillance aircraft,” the statement said.

“He was due back in Albuquerque that August 1. But after leaving for Europe, he was never seen again. On December 9, 1983, the Air Force formally declared him a deserter.”

Investigators interviewed friends, associates and coworkers, along with international law enforcement officials after Captain Hughes’ disappearance, but were unable to find him.

His family at one point theorised he had been abducted.

Captain Hughes is charged with desertion and is being held at Travis Air Force Base in California, the Associated Press reported.

Neighbor Lorenzo Laurel, 62, told the AP that Captain Hughes was an “ideal neighbour”.

“I would only see him when he leaves or throws out the garbage, he was very private,” Mr Laurel, who never knew his neighbour’s occupation and assumed he was retired, was quoted as saying.

There are several other fugitives on the Air Force’s wanted list, including others who have been on the run since the 1980s for various reasons ranging from drug charges to security issues, the AP said.

Investigators last year caught a fugitive in Florida who had been living under another identity since 1972.

-with agencies