A regular US air force unit based in the Nevada desert is responsible for flying the CIA's drone strike programme in Pakistan, according to a new documentary to be released on Tuesday.

The film – which has been three years in the making – identifies the unit conducting CIA strikes in Pakistan's tribal areas as the 17th Reconnaissance Squadron, which operates from a secure compound in a corner of Creech air force base, 45 miles from Las Vegas in the Mojave desert.

Several former drone operators have claimed that the unit's conventional air force personnel – rather than civilian contractors – have been flying the CIA's heavily armed Predator missions in Pakistan, a 10-year campaign which according to some estimates has killed more than 2,400 people.

Hina Shamsi, director of the American Civil Liberties Union's National Security Project, said this posed questions of legality and oversight. "A lethal force apparatus in which the CIA and regular military collaborate as they are reportedly doing risks upending the checks and balances that restrict where and when lethal force is used, and thwart democratic accountability, which cannot take place in secrecy."

The Guardian approached the National Security Council, the CIA and the Pentagon for comment last week. The NSC and CIA declined to comment, while the Pentagon did not respond.

The role of the squadron, and the use of its regular air force personnel in the CIA's targeted killing programme, first emerged during interviews with two former special forces drone operators for a new documentary film, Drone.

Brandon Bryant, a former US Predator operator, told the film he decided to speak out after senior officials in the Obama administration gave a briefing last year in which they said they wanted to "transfer" control of the CIA's secret drones programme to the military.

Bryant said this was disingenuous because it was widely known in military circles that the US air force was already involved.

"There is a lie hidden within that truth. And the lie is that it's always been the air force that has flown those missions. The CIA might be the customer but the air force has always flown it. A CIA label is just an excuse to not have to give up any information. That is all it has ever been."

Referring to the 17th squadron, another former drone operator, Michael Haas, added: "It's pretty widely known [among personnel] that the CIA controls their mission."

Six other former drone operators who worked alongside the unit, and who have extensive knowledge of the drone programme, have since corroborated the claims. None of them were prepared to go on the record because of the sensitivity of the issue.

Bryant said public scrutiny of the programme had focused so far on the CIA rather than the military, and it was time to acknowledge the role of those who had been carrying out missions on behalf of the agency's civilian analysts.

"Everyone talks about CIA over Pakistan, CIA double-tap, CIA over Yemen, CIA over Somalia. But I don't believe that they deserve the entirety of all that credit for the drone programme," he said. "They might drive the missions; they might say that these are the objectives – accomplish it. They don't fly it."

Another former drone operator based at Creech said members of the 17th were obsessively secretive.

"They don't hang out with anyone else. Once they got into the 17th and got upgraded operationally, they pretty much stopped talking to us. They would only hang out among themselves like a high school clique, a gang or something."

Shamsi said the revelations, if true, raised "a host of additional pressing questions about the legal framework under which the targeted killing programme is carried out and the basis for the secrecy that continues to shroud it."

She added: "It will come as a surprise to most Americans if the CIA is directing the military to carry out warlike activities. The agency should be collecting and analysing foreign intelligence, not presiding over a massive killing apparatus.

"We don't know precisely what rules the CIA is operating under, but what we do know makes clear that it's not abiding by the laws that strictly limit extrajudicial killing both in and out of traditional battlefields. Now we have to ask whether the regular military is violating those laws as well, under the secrecy that the CIA wields as sword and shield over its killing activities.

"Congressional hearings in the last year have made it embarrassingly clear that Congress has not exercised much oversight over the lethal programme."

In theory, the revelation could expose serving air force personnel to legal challenges based on their direct involvement in a programme that a UN special rapporteur and numerous other judicial experts are concerned may be wholly or partly in violation of international law.

Sitting 45 miles north-west of Las Vegas in the Mojave desert, Creech air force base has played a key role in the US drone programme since the 1990s.

The 432d wing oversees four conventional US air force Predator and Reaper squadrons, which carry out surveillance missions and air strikes in Afghanistan.

There is another, far more secretive cluster of units within the wing called the 732nd Operations Group, which states that it "employs remotely piloted aircraft in theatres across the globe year-round".

This operations group has four drone squadrons, which all appear to be linked with the CIA.

The 30th Reconnaissance Squadron "test-flies" the RQ-170 Sentinel, the CIA's stealth drone which made headlines after one was captured over Iran in December 2011.

The 22nd and 867th Reconnaissance Squadrons each fly Reaper drones, the more heavily armed successor to the Predator.

But it is the last of the four units – the 17th Reconnaissance Squadron – that is now under the most scrutiny.

It is understood to have 300 air crew and operates about 35 Predator drones – enough to provide five or six simultaneous missions during any 24-hour period.

It operates from within an inner compound at Creech, which even visiting military VIPs are unable to access, say former base personnel. Former workers at Creech say the unit was treated as the "crown jewels" of the drone programme.

"They wouldn't even let us walk by it, they were just so protective of it," said Haas, who for two years was a drone operator. He was also an operational trainer at Creech.

"From what I was able to gather, it was pretty much confirmed they were flying missions almost exclusively in Pakistan with the intent to strike."

In the Operations Cell, which receives video feeds from every drone "line" in progress at Creech, mission co-ordinators from the 17th were kept segregated from all the others.

Established as a regular drone squadron in 2002, the unit transitioned to its new "customer" in 2004 at the same time that CIA drone strikes began in Pakistan, former personnel have said.

The operators receive their orders from civilian CIA analysts who ultimately decide whether – and against whom – to carry out a strike, according to one former mid-level drone commander.

Creech air force base would only confirm that the 17th squadron was engaged in "global operations".

"The 732nd Operations Group oversees global operations of four squadrons – the 17th Reconnaissance Squadron, 22nd Reconnaissance Squadron, 30th Reconnaissance Squadron and the 867th Reconnaissance Squadron. These squadrons are all still active … their mission is to perform high-quality, persistent, multi-role intelligence, surveillance, and reconnaissance in support of combatant commanders' needs."

Although the agency's drone strikes have killed a number of senior figures in al-Qaida and the Taliban, the CIA also stands accused by two United Nations investigators of possible war crimes for some of its activities in Pakistan. They are probing the targeting of rescuers and the bombing of a public funeral.

• Tonje Schei's film Drone premieres on Arte on 15 April.

• Chris Woods is the author of Sudden Justice: America's Secret Drone Wars, which is published next winter in the US and Europe.