"I'm not at liberty to discuss that," he said. "But we took a very comprehensive approach. Nothing was too small to investigate."
He added: "In my opinion, if this was a court of law, we have reached the point of 'beyond reasonable doubt'. I hate to use the term UFO but that's what were looking at.
"I think it's pretty clear this is not us, and it's not anyone else, so one has to ask the question where they're from."
The exact number of UFO sightings investigated, and witnesses interviewed, is also classified but Elizondo said there had been "lots".
Geographical "hotspots" emerged during the investigations, sometimes near nuclear facilities and power plants.
Common factors between the movements of separate unidentified objects had also been identified by the Pentagon team.
"It was enough where we began to see trends and similarities in incidents," he said.
"There were very distinct observeables. Extreme manoeuvrability, hypersonic velocity without a sonic boom, speeds of 7-8000m/h (11,265-12,875km/h), no flight surfaces on the objects. A lot of this is backed with radar signal data, gun camera footage from aircraft, multiple witnesses.
"There was never any display of hostility but the way they manoeuvred, in ways no one else in the world had, you have to be conscious something could happen."
After the existence of the secret programme was revealed, attention focused on the release of footage of an unidentified object off San Diego in 2004.
Commander David Fravor, a US navy pilot flying an FA-18 near the object, described seeing a "white Tic Tac, about 40ft (12m) long with no wings" which was "something not from the Earth".
Elizondo said Commander Fravor was a "national hero" for speaking out.
He said: "The social stigma about this is unbelievable, it's very challenging. There are many other Commander Fravors out there who have come forward (to us), but he's brave enough to discuss his experience publicly."
Elizondo said he had no preconceived ideas when he took the helm of the Pentagon programme, but later became convinced by what he saw.
"We [career intelligence officers] tend to be sceptics by nature. For some of us working on it the time came as an 'Aha!' moment, for others it was a slow progress towards the realisation that these are probably not any type of aircraft in any national inventory.
"I don't want to pre-suppose where they're from. We were looking at two things: What is it? How does it work?
"As to who's behind the wheel, and why is it here, that will fall into place. I think it's pretty clear it's not us, and it's not anyone else.
"What we were trying to do was basically take the voodoo out of voodoo science."
He refused to confirm or deny whether any technology had been recovered from any of the objects investigated.
However, buildings were modified by a private contractor in Nevada as a place to store anything discovered linked to the UFO incidents.
Witnesses to UFO sightings were also examined to see if there had been any physical effects on them.
Elizondo said his team had developed theories about what was propelling the objects.
"There are some tell tale clues," he said. "We are getting to how it works, that's a significant step."
Despite the Pentagon saying funding for AATIP ended in 2012, Elizondo said his team's UFO work carried on for another five years.
"When you're given a mission you guard your post until you're relieved of responsibility, and that never came for us," he said.
"There was an expectation that you continue to do what you're doing."
He eventually resigned in October, frustrated at excessive secrecy surrounding the programme.
In a resignation letter to Jim Mattis, the Defence Secretary, he wrote: "Why aren't we spending more time and effort on this issue? There remains a vital need to ascertain capability and intent of these phenomena for the benefit of the armed forces and the nation."
Elizondo told the Telegraph: "I'd say bolster the programme. We want Nasa to find life on different planets, but we have highly educated pilots here and they're seeing something they can't understand."
