Only a small number of officials were aware of the programme, which began in 2007 and was reportedly closed in 2012.
But scientists were doubtful, stressing that unexplained happenings were not necessarily proof of alien life.
The Advanced Aerospace Threat Identification Programme was the brainchild of Harry Reid, a retired Democratic senator who was the Senate majority leader at the time.
He told the New York Times: “I’m not embarrassed or ashamed or sorry I got this thing going. I’ve done something that no one has done before.”
The programme is reported to have cost the Department of Defense more than $20 million (£15m) before it was shut down in order to save costs.
Although its funding ended in 2012, officials have reportedly continued to investigate sightings of unusual aerial phenomena and suspicious objects alongside their daily duties.
“Was this China or Russia trying to do something or has some propulsion system we are not familiar with?”, they said.
Earlier this year, the US Central Intelligence Agency (CIA) released millions of pages of declassified documents online.
The records included UFO sightings and a collection of reports on flying saucers. (Courtesy BBC)