Although the Advanced Aviation Threat Identification Programme ended five years ago, when US defence officials shifted attention and funding to other priorities, it remains unclear if it has continued to investigate sightings of mysterious vehicles.
The programme ran from 2007 to 2012 with $22m (£15m) in annual funding, which was hidden in US Defence Department budgets worth hundreds of billions of dollars, The New York Times reported.
Initial funding came largely at the request of former Senate Democratic leader Harry Reid, the Nevada Democrat long known for his enthusiasm for space phenomena, the newspaper said.
Most of the money went to an aerospace research company ran by Robert Bigelow, a billionaire entrepreneur and longtime friend of Mr Reid.
"I’m not embarrassed or ashamed or sorry I got this thing going," Mr Reid told The New York Times.
But according to its backers, the programme remains in existence and officials continue to investigate UFO episodes brought to their attention by service members alongside their other duties, the paper said.
A former congressional staffer told the Politico news website that the programme may have been established to monitor whether a rival foreign power had developed potentially threatening next-generation technology.
"Was this China or Russia trying to do something or has some propulsion system we are not familiar with?" they asked.
The Pentagon openly acknowledged the fate of the programme.
"The Advanced Aviation Threat Identification Programme ended in the 2012 timeframe," Laura Ochoa, a spokeswoman said. "It was determined that there were other, higher priority issues that merited funding and it was in the best interest of the Department of Defence to make a change.
But the Pentagon was less clear about whether the programme has continued since then.
"The DoD takes seriously all threats and potential threats to our people, our assets, and our mission and takes action whenever credible information is developed," Ms Ochoa said.
In a tweet linking to the New York Times story, Mr Reid wrote: "The truth is out there. Seriously."
He added: "If anyone says they have the answers, they’re fooling themselves. We don’t know the answers but we have plenty of evidence to support asking the questions. This is about science and national security.
"If America doesn’t take the lead in answering these questions, others will."
The Pentagon has admitted it ran a secret programme tasked with investigating sightings of unidentified flying objects, or UFOs.