The program has countless videos of UFO encounters by military personnel, as well as interview about firsthand accounts, physiological studies of those who've come into contact with odd crafts, and possibly even samples of unusual technology.
Reid confirmed the existence of the program, as did Pentagon officials, though the latter claim that the program ended in 2012.
Until his departure the program, though unclassified, had nevertheless been a Pentagon secret in that its existence had never been publicly acknowledged.
The New York Times reported on Saturday that the hush-hush program, tasked with investigating sightings of unidentified flying objects, or UFOs, ran from 2007 to 2012 with $22 million in annual funding secretly tucked away in U.S. Defense Department budgets worth hundreds of billions of dollars.
Former senate majority leader and retired Nevada lawmaker Harry Reid was AATIP's catalyst, earmarking over $20 million of the defense department's budget to fund it. Billionaire Robert Bigelow's aerospace company secured numerous program's early contracts.
However, Elizondo said that even without its generous funding, the program was still alive, telling the New York Times that he was working with Central Intelligence Agency and Navy officials on the issue up to his resignation.
Pentagon confirmed existence of UFO program, incident videos released
"It was determined that there were other, higher priority issues that merited funding, and it was in the best interest of the DoD to make a change", Pentagon spokesperson Thomas Crosson told the Times.
From 2008 to 2011, Bigelow Aerospace landed almost $22 million for Congress for the purposes of its extensive research and evaluating threats coming from the objects, according to the contracts cited by the paper.
In one eerie encounter, a whitish oval object, about the size of a commercial plane, was chased by two Navy F/A-18F fighter jets from the aircraft carrier Nimitz off the coast of San Diego.
Elizondo was clearly a fan of AATIP too, and hasn't given up on UFO research. The detailed account of the encounter was given by Chris Mellon, a former member of Senate Intelligence Committee, who is engaged in a new initiative, spearheaded by Elizondo, called To the Stars Academy of Arts & Science. Elizondo told reporters that he did have a successor, though he couldn't name them.
Also tweeting a link to the article, Mr Reid's former spokeswoman Kristen Orthman said: "If you've talked to Harry Reid for 60 seconds then it's the least surprising thing ever that he loves UFOs and got an earmark to study them". "I've done something that no one has done before". "I've done something that no one has done before".
"There was really nothing there that we could justify using taxpayer money", the unnamed official said.