WASHINGTON — In the $600 billion annual Defense Department budgets, the $22 million spent on the Advanced Aerospace Threat Identification Program was almost impossible to find.

Which was how the Pentagon wanted it.

For years, the program investigated reports of unidentified flying objects, according to Defense Department officials, interviews with program participants and records obtained by The New York Times. It was run by a military intelligence official, Luis Elizondo, on the fifth floor of the Pentagon’s C Ring, deep within the building’s maze.

The Defense Department has never before acknowledged the existence of the program, which it says it shut down in 2012. But its backers say that, while the Pentagon ended funding for the effort at that time, the program remains in existence. For the past five years, they say, officials with the program have continued to investigate episodes brought to them by service members, while also carrying out their other Defense Department duties.

The shadowy program — parts of it remain classified — began in 2007, and initially it was largely funded at the request of Harry Reid, the Nevada Democrat who was the Senate majority leader at the time and who has long had an interest in space phenomena. Most of the money went to an aerospace research company run by a billionaire entrepreneur and longtime friend of Mr. Reid’s, Robert Bigelow, who is currently working with NASA to produce expandable craft for humans to use in space.