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WASHINGTON (CNN/WNCN) – The New York Times reported over the weekend on a once-classified multi-million dollar Pentagon program that examined the possible existence of UFOs.

According to the Times, the program’s research included recordings of aerial encounters by military pilots and unknown objects.

Commander David Fravor still can’t explain what he says he saw that day.

In November 2004, the Navy fighter-pilot was on a training mission west of San Diego when he was ordered to check out something in the water, not far away.

On a clear day, over a smooth ocean – he saw the object – waves breaking over it – and says he saw something hovering above it.

“It’s randomly moving, North, South, East, West, just random. Just stopping, going the other direction. Like you could do with a helicopter, but a little bit more abrupt. It looks like a 40-foot long tic-tac, with no wings,” Fravor said in a newly-released video of the encounter.

Fravor says he and his four-man team tracked the object for several minutes, until it just disappeared.

CNN has learned the Pentagon had a secretive program to research UFOs like the one Fravor spotted.

The projected was called the Advanced Aviation Threat Identification Program – run by an official named Luis Elizondo.

“I think this is a national security imperative. We have clear things that we do not understand how they work, operating in areas that we can’t control,” said Elizondo.

A defnse official told CNN the program cost at least $22 million over five years, before it was shut down in 2012.

According to the New York Times and Politico, which fire reported this story, tens of millions of dollars for the project were pushed through by former Senate Majority Leader Harry Reid.

Those publications say a lot of the money for the Pentagon UFO program went to a company called Bigelow Aerospace, run by a longtime friend of Reid’s, Robert Bigelow – a big believer in UFOs.

Public records show Bigelow contributed about $20,000 to Reid and his Political Action Committee.

“That that campaign contributor got research contracts from this program: that just is a bad picture. It doesn’t look good for anybody. It’s hard to imagine that something that came about that way and profited somebody who pushed for the program was a good use of taxpayer money,” said Ryan Alexander, with Taxpayers for Common Sense.

A Pentagon spokesman, in fact, told CNN the program was shuttered because there were “Other, higher priority issues that merited funding.”

“It’s definitely crazy to spend $22 million to research UFOs. Pilots are always going to see things that they can’t identify, and we should probably look into them. But to identify them as UFOs, to target UFOs to research- that is not the priority we have as a national security matter right now,” Alexander said.

But pilots, like Fravor, who says he saw something – see merits in the program.

“What if it is real – because I think it’s real because I saw it – and what if there’s more of these, and what if we do nothing?” Fravor asked.

Reid tells CNN that he’s “proud of the program,” and that it’s counterproductive to politicize the serious questions the program raised.

Robert Bigelow did not initially respond to CNN’s requests for comment on the story.

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