Luis Elizondo, who quit as head of the Advanced Threat Identification Programme (AATIP) two months ago, warned nations now "had to be conscious" of the potential threat posed by UFOs.
The unit, which the Department of Defence (DoD) insisted was terminated in 2012, produced documents that described sightings of aircraft travelling at extremely high speeds with no visible signs of propulsion.
"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 we're looking at," Mr Elizondo told The Telegraph.
"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."
Mr Elizondo told the newspaper there were geographical "hot spots" – sometimes around nuclear facilities and power plants – which emerged during AATIP's investigations, as well as common factors between UFO sightings.
He said: "It was enough where we began to see trends and similarities in incidents. There were very distinct observables. Extreme manoeuvrability, hypersonic velocity without a sonic boom, speeds of 7,000mph to 8,000mph, 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."
It comes after secret footage released by the Department of Defence (DoD) showed US fighter jet pilots as they tracked an unidentified aerial object gliding above the Pacific Ocean in 2004. The object had been detected appearing suddenly at 80,000 feet by the USS Princeton, a naval cruiser, which had been tracking mysterious aircraft for two weeks.
Commander David Fravor told The New York Times the object was about 40ft long, had no plumes, wings or rotors, and outpaced their F-18s. It was big enough to churn the sea 50ft below it, he said.
"I have no idea what I saw ... It accelerated like nothing I've ever seen," he added, admitting he was "pretty weirded out".
Mr Elizondo described Mr Fravor as a "national hero" for speaking out due to the "social stigma" attached to UFO sightings by military personnel.
He said he had no preconceived ideas when he first took charge of the unit, but came to realise there were "probably not any type of aircraft in any national inventory" similar to the sightings.
"I think it's pretty clear it's not us, and it's not anyone else," he added.
Mr Elizondo quit AATIP in October over what he believed was excessive secrecy surrounding the programme.
In a resignation letter to James Mattis, the US 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."
Experts warn there is usually a worldly explanation for apparent UFO sightings and caution that an absence of an explanation is not proof of aliens.
The Pentagon said AATIP closed five years ago when defence officials shifted funding to other priorities. But according to its backers, it remains in existence in some form.
"The AATIP ended in the 2012 timeframe," Pentagon spokesperson Laura Ochoa said. "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," she added.
Asked if the department continued to investigate sightings, she said: "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."
The existence of unidentified flying objects using technology more advanced than human capabilities has been proved "beyond reasonable doubt", the former head of a secret US government programme has said.