A senior strategic analyst has called for the Federal Government to rethink the Pine Gap communications facility, saying some of its work now is "ethically unacceptable".

Australian National University Professor Des Ball previously supported the joint Australia-US communications facility near Alice Springs, but changes to its role since the Al Qaeda attacks in 2001 have changed his mind.

"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," he said.

Pine Gap is the jewel in the crown of Australia-US intelligence sharing, detecting nuclear weapons and intercepting communications around the globe.

But for the past decade it has also been involved in the US drone program, which has killed thousands of militants and some civilians in countries including Afghanistan, Pakistan, Yemen, Somalia and Iraq.

"We're now locked into this global network where intelligence and operations have become essentially fused," Professor Ball told 7.30.

"And Pine Gap is a key node in that 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."

Former Pine Gap analyst says base is 'vital'

Pine Gap began operating in 1970 and is partly managed by the CIA and the US National Security Agency.

It has always been controversial and the 1980s saw anti-nuclear protesters converge on the desert site demanding its closure.

Twenty years later, it was anti-Iraq war protesters calling for the same thing.

Professor Ball was the first to publicly reveal the site's existence and over the decades has kept a close watch on its activities.

In 1987 he argued that Pine Gap's monitoring of Soviet weapons development was crucial to keeping a check on the arms race.

Former US intelligence analyst David Rosenberg worked at Pine Gap for 18 years and has written a book about his experience – the only insider's description of the base.

He disagrees with Mr Ball's current assessment.

"I believe that Pine Gap is very vital to Australia," he told 7.30.

"It collects intelligence that may not be accessible from very many sources.

"Sometimes Pine Gap is a sole source of collection of some intelligence and that can, of course, be used to safeguard our troops, our people here in Australia, in the United States and our allies as well."

Following the Al Qaeda attacks on the US in 2001, Pine Gap's role changed, with its focus switched from monitoring nuclear proliferation to countering terrorism.

"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, are being fed from intelligence sources like Pine Gap – still one of the two biggest stations of this sort in the world – and we're thoroughly embedded into it," Professor Ball said.

Use of drones marks new era of 'information warfare': Ball

In November, 2001, the US launched its first armed Predator drone as part of the hunt for Al Qaeda leaders in Afghanistan, marking the beginning of a new era.

"It's now information warfare," Professor Ball said.

"It's now using data directly from sensors, the satellites above, down to Pine Gap and directly to the shooters."

Mr Rosenberg left Pine Gap in 2008 and soon afterwards the new Obama administration in the US ordered a major escalation in the use of drone strikes.

He says the US should use whatever information is available to it.

"If the US military could make use of whatever assets it has in place to help the drone program, then the US military would, of course, do that," he said.

"I think that when you look at Pine Gap and all of its capabilities, it does have a vast electronic collection capability, and whatever signals Pine Gap can collect that could be of use to the government will certainly be passed on."

And that is what is causing Professor Ball concern.

"The drone program puts some of these dilemmas on a plate in front of you," he said.

"You have to start confronting this conflation of intelligence and operations, which has been an ongoing process now for some time.

"But the drones bring it right out in front, including on your television sets, and including the fact that I don't know either how many terrorists have been killed by drones.

"But I would not be surprised if the total number of children exceeds the total number of terrorists. I don't know."

And he fears support of lethal US operations is becoming a steadily increasing part of what Pine Gap does.

"Aspects of what is collected there, the general surveillance function expanding, and the now increasing military operational uses, 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."