The Pentagon has admitted that, up until 2012, it was running a long-secret investigation into unidentified flying objects, or UFOs.

The multi-million-dollar investigation was kept hush-hush from when it was established in 2007 up until 2012.

The program was allocated $US22 million in annual funding secretly tucked away in US Defence Department budgets worth hundreds of billions of dollars.

Its initial funding came largely at the request of former Democratic senator Harry Reid, the Nevada politician long known for his enthusiasm for space phenomena.

The New York Times reported most of the money went to a space research company run by the billionaire Robert Bigelow, who is convinced that aliens exist.

This infrared footage from the Mexican Air Force purportedly shows a close encounter with UFOs. ( Reuters )

According to its backers, the newspaper reported, the program remains in existence and officials continue to investigate UFO episodes brought to their attention by service members.

The Pentagon acknowledged the fate of the program, saying: "The Advanced Aerospace Threat Identification Program ended in the 2012 timeframe."

"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 spokeswoman Laura Ochoa said in the statement.

But the Pentagon was less clear about whether the UFO program continues to hover somewhere in the vast universe of the US Defence establishment.

Earlybirds along Australia's east coast were startled by a bright spiral moving across the sky in June, 2010. ( Craig Boyce: User submitted )

"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," Ms Ochoa said.

Documents from the programs describe sightings of unidentified objects speeding through the skies or hovering with no visible signs of lift.

Scientists have stressed that unexplained phenomena are not proof of inter-stellar visitors.

A north Queensland man said he and his son watched these two points of light hover in the night sky above Cardwell for 15 minutes. ( Audience submitted: Greg Smith )

Responding to the New York Times, Mr Reid tweeted the truth was out there and the investigation was about science and national security.

"We don't know the answers but we have plenty of evidence to support asking the questions," Mr Reid tweeted.

"This is about science and national security. If America doesn't take the lead in answering these questions, others will."

This image shows an unidentified object above southern Tasmania in February, 2017. ( Supplied )

ABC/Reuters