CHRIS UHLMANN, PRESENTER: For almost half a century, the joint US-Australian defence base at Pine Gap has lurked on the edge of our consciousness in the Northern Territory desert, mostly accepted, but largely mysterious.

The little we know is that it scoops up secrets from satellites that watch nuclear weapons stockpiles and spy on foreign governments.

But now there are claims it has a new role in the post 9-11 world, directing American drone strikes that have killed thousands of militants and civilians over the last five years.

And that has led Australia's pre-eminent intelligence expert and former cheerleader for the site to brand some of its work "ethically unacceptable".

Dylan Welch reports.

DYLAN WELCH, REPORTER: With a few small steps and some gladhanding, the US launched its latest charm offensive designed to further strengthen military co-operation between Australia and the United States.

CHUCK HAGEL, US SECRETARY OF DEFENSE: I very much appreciate the opportunity to renew our friendship and be together again. And I'm particularly pleased to be back in Australia.

DYLAN WELCH: Deep in Australia's Outback and shrouded in secrecy lies the base that's been at the centre of that relationship for decades.

Pine Gap is the jewel in the crown of US-Australian intelligence sharing, detecting nuclear weapons and intercepting communications around the globe. For a decade, it's also been involved in the US drone program, which has killed thousands of militants and some civilians in countries including Pakistan, Afghanistan, Yemen, Somalia and Iraq.

Now Australia's pre-eminent intelligence expert says Pine Gap's role has gone too far.

DES BALL, STRATEGIC & DEFENCE STUDIES CENTRE, ANU: I've reached the point now where I can no longer stand up and provide the verbal, conceptual justification for the facility that I was able to do in the past. We're no linked in to this global network where intelligence and operations have become essentially fused and Pine Gap is a key node in that whole network, that war machine, if you want to use that term, which is doing things which are very, very difficult, I think, as an Australian, to justify.

DYLAN WELCH: Pine Gap has intrigued outsiders ever since it was set up by the US and Australian governments and began operating in 1970.

It's managed partly by America's CIA and National Security Agency and controls US spy satellites orbiting around the globe.

MALE VOICEOVER (archive footage): High above the Earth, the spy satellites can monitor everything. Missile silos, ship movements, aircraft, radar, electronic signals - nothing escapes their antennae or their lenses.

DYLAN WELCH: Pine Gap has always been controversial. In the 1980s, anti-nuclear protestors converged on the desert site to demand the closure of the base.

20 years later, demonstrators campaigning against the Iraq War descended on the base again.

It was Des Ball who revealed Pine Gap's existence in 1969, and over decades, has kept a close watch on its activities. In 1987, he argued Pine Gap's monitoring of Soviet weapons development was crucial to keeping a check on the arms race.

DES BALL (archive footage, 1987): Since that monitoring function is quite critical to most of the kind of arms control agreements which are in force between the United States and Soviet Union, you wouldn't have those arms control agreements without Pine Gap.

DYLAN WELCH: Former US intelligence analyst David Rosenberg worked at Pine Gap for 18 years. He wrote Inside Pine Gap, which remains the only insider's description of the base.

DAVID ROSENBERG, US INTELLIGENCE ANALYST, PINE GAP (1990-2008): I believe that Pine Gap is very vital to Australia. It collects intelligence that may not be accessible from very many other sources. Sometimes Pine Gap is a sole source of collection of some intelligence and that of course can be used to safeguard our troops, to safeguard our people here in Australia and in the United States and our allies as well.

DYLAN WELCH: Following the al-Qaeda attacks of 2001, Pine Gap's role changed as its focus switched from monitoring nuclear proliferation to countering terrorism and Des Ball grew increasingly concerned.

DES BALL: We're entering - we've already entered into a new phase of warfare where intelligence and unmanned vehicles of various sorts - under the water, killer satellites in space, battlefield, being fed from intelligence sources like Pine Gap, still one of the two biggest stations of the sort in the world, and we're thoroughly embedded into it.

DYLAN WELCH: In November, 2001, the US launched its first armed Predator drone as part of the hunt for al-Qaeda leaders in Afghanistan. It marked the beginning of a new era.

DES BALL: It's now information warfare, it's now using data directly from censors, the satellites up above, down to Pine Gap, but directly to the shooters.

DYLAN WELCH: Rosenberg left Pine Gap in 2008. Soon after, the new Obama administration ordered a major escalation in the use of drone strikes.

DAVID ROSENBERG: If the US military could make use of whatever assets it has in place to help the drone program, then the US military will of course do that. Whatever signals Pine Gap can collect that could be of use to the governments would certainly be passed on.

DYLAN WELCH: After decades of watching and supporting Pine Gap, Ball finds its key role in the drone program deeply concerning.

DES BALL: The drone program puts some of these dilemmas on a plate in front of you. You have to start confronting this conflation of intelligence and operations. I don't know how many terrorists have been killed either by drones, but I would not be surprised if the total number of children exceeds the total number of terrorists.

DYLAN WELCH: And Des Ball fears support of lethal US operations is becoming a steadily increasing part of what Pine Gap does.

DES BALL: If they were really to change the balance around so that Pine Gap basically became a war-fighting machine rather than an intelligence collector, then I think we all have to have second thoughts.

CHRIS UHLMANN: Dylan Welch reporting.