Last week, the Australian reported the involvement of Australian soldiers in what it called "a targeted assassination".

The journalist Mark Dodd detailed how Australian forces had killed Mullah Noorullah — described as a "senior Taliban leader" — in the Deh Rafshan district in Southern Oruzgan, where the Australian Special Operations Task Group is based. Dodd added: "The SOTG tag is commonly used by defence as a synonym to describe elite [Australian] Special Air Service operatives authorised to hunt and kill Taliban leaders in an Afghan variation on the Vietnam-era Phoenix Program."

Nowhere is the parochialism of the local media more apparent than in coverage of Australian troops in combat (the Daily Telegraph advertised the same story with the headline: "Elite Aussie troops claim another top Taliban scalp") but even so, you would have expected some more alarm at the revelation that Australian troops were not only engaged in assassinations but were also openly modelling their campaign on Phoenix, the notorious CIA program of murder and torture.

The original Phoenix Program emerged in the mid-1960s when the CIA organised Vietnamese troops into Provincial Reconnaissance Units (PRUs) to neutralise (that is, capture or kill) the members of the civilian cadre supporting the Vietcong’s alternative government in South Vietnam. By 1971, a US House Operations Subcommittee investigation heard the CIA’s William Colby acknowledge that in three years from 1968, Phoenix killed 20,587 Vietnamese civilians — though the New York Times independently estimated the figure at more like 60,000.

Ted Serong — a former Australian army officer who joined the CIA — played a leading role in all of this. Sarong always defended Phoenix. "Yes," he said, "we did kill teachers and postmen. But it was the way to conduct the war. They were part of the Viet Cong Infrastructure. I wanted to make sure we won the battle."

Such testimony made the Phoenix Program synonymous with atrocity — an operation that, for many years, America preferred to forget. So why is Phoenix now deemed worthy of emulation?

In an article on the program for the military journal Joint Force Quarterly, Mark Moyar of the US Marine Corps University explained: "In the mid-1990s, the Phoenix program was considered an artifact of historical interest but with little relevance to the contemporary world. […] A decade later, Iraq and Afghanistan have brought the study of counter-insurgency and counter-terrorism back into fashion."

With those wars proceeding so badly, any strategies claiming to have "won the battle" against insurgents became suddenly attractive. Another Australian, the soldier and academic Lieutenant Colonel David Kilcullen, argued in a 2004 paper for the Small Wars Journal that Phoenix had been "unfairly maligned". It was, he argued, essentially a "civilian aid and development program", backed by largely successful operations intended to destroy the Vietcong’s infrastructure in rural areas of South Vietnam. Furthermore, he said, the War on Terror required a "global Phoenix Program".

It was not idle talk. Kilcullen has become one of the most influential theorists in the area, serving as senior adviser on counterinsurgency to General David Petraeus (architect of the Iraq "surge"), a special advisor for counter-insurgency to Condoleezza Rice and chief counterterrorism strategist for the US State Department.

In a 2006 article in Military Review, the military writers Dale Andrade and Lieutenant Colonel James Willbanks spelled out the lessons counterinsurgency specialists are now taking from the Phoenix experience. Like Kilcullen, they insist that the Vietnam program was largely successful. As evidence they draw on the testimony of the Vietcong, quoting, for instance, the former Vietcong Minister of Justice Truong Nhu Tang as saying that "Phoenix was dangerously effective". Today, they argue, Western forces engaged in counterinsurgency must once again work with locals, Phoenix-style, in a concerted campaign to eliminate the insurgent infrastructure.

That seems to be the modus operandi of the SOTG program. In the wake of the Mullah Noorullah killing, the Defence Department explained that its assassinations were "designed to disrupt" the Taliban, forcing them to divert time to recruiting and training new members. Yet today’s advocates of Phoenix prefer not to discuss the atrocities that enabled its "successes" in Vietnam.

Since the assassination of non-uniformed civilians depends upon the accurate identification of targets, intelligence collation was fundamental to Phoenix, and so the creation of the Provincial Reconnaissance Units was accompanied by the construction of regional interrogation centres at which suspected Vietcong could be interrogated. But, to successfully neutralise Vietcong supporters, the CIA not only wanted prisoners to talk but it also wanted them to talk quickly, before their information became out of date. So, from the very beginning, Phoenix utilised what today’s military officials describe with the obscene euphemism "coercive interrogations".

Moyar’s account makes clear the connection between Phoenix’s "achievements" and torture:

"Some American witnesses contended that the use of torture did not cause Communist prisoners to divulge accurate information. Many others, however, including all of the South Vietnamese veterans with whom I spoke, contended that torture did yield valuable information. These findings support the view, espoused in some current debates over the handling of terrorists, that coercive interrogation can achieve results that other forms cannot. Interrogators with extensive training in the techniques of their trade frequently succeeded in extracting information through kind treatment and rewards. The benevolent approach, which many Americans favoured, often induced prisoners to share more information than tortured prisoners would generally yield — but it took longer than other methods, and thus the information sometimes lost its value by the time the interrogators elicited it."

As Moyar hints, the renewed interest in Phoenix with the onset of the War on Terror related directly to its employment of torture. Writing in the New Yorker, Jane Mayer quotes CIA operatives discussing how, in their search for "dark side" methods, they returned to the files on Phoenix.

As well, Michael Otterman’s book American Torture contains a lengthy discussion of Phoenix, as part of his argument about the continuity of CIA torture: the techniques taught to the (mostly) South Vietnamese interrogators working for Phoenix (waterboarding, stress positions, exposure to extreme cold, sleep deprivation, sensory isolation and so on) were transmitted to another generation at Guantánamo Bay, Abu Ghraib and Bagram Air Base.

Yet the "scientific" tortures pioneered by the Americans were only ever one aspect of Phoenix’s atrocities, for the CIA allowed its local allies considerable latitude for innovation. In 1968, an official Pentagon investigation concluded that "the truncheon and electric shock method of interrogation were in widespread use, with almost all [US] advisors admitting to have witnessed instances of the use of these methods". The Phoenix interrogators employed the official slogan "Khong, danh cho co’". ("If they are innocent, beat them until they become guilty".) A historian from the US Naval Institute acknowledged that "the large majority of South Vietnamese interrogators tortured some or all of the communist prisoners in their care".

Indeed, Kenneth Barton Osborn, an army military intelligence officer who worked with Phoenix in 1967 and 1968 flatly told the US House Operations Subcommittee that not a single VC suspect survived interrogation under his supervision. He discussed two of the murders that he witnessed personally: on one occasion, a piece of wood was inserted into the ear canal of a detainee and hammered into his brain; in another, a woman was simply left in a small cage to starve to death.

If there is no evidence that Australian troops in Afghanistan engage in the vile acts Osborn describes, there is a great deal of evidence that the forces with which they are allied often do. Amnesty International has documented how Afghanistan’s National Directorate of Security subjects its detainees to "torture and other ill-treatment, including being whipped, exposed to extreme cold and deprived of food".

In a frank submission to the United Nations Human Rights Council, the Government of Afghanistan itself acknowledged that "torture and cruel treatment is common" in its detention facilities, while a recent report suggested that less than 20 per cent of Afghan officials actually knew that torturing suspects was illegal.

And why should they? After all, President Hamid Karzai is running for re-election in forthcoming elections alongside a man called Mohammad Qasim Fahim, described by Human Rights Watch as "one of the most notorious warlords in the country, with the blood of many Afghans on his hands". In such circumstances, it is hard to see how an assassination program — presumably dependent upon information gathered from the local security forces — could avoid complicity with human rights violations.

The disturbing implications of what it means to employ these methods go even deeper. The accounts of Phoenix suggest — not surprisingly — that the program inculcated in its personnel a generalised indifference to human life. After all, its focus on neutralising civilians meant that Phoenix operated, by definition, outside the Geneva Conventions.

The situation in Afghanistan is more ambiguous. What exactly is the Taliban infrastructure that the SOTG assassinations target? On what basis are those belonging to it selected to be killed? We already know that, on one occasion, Australian commandos, presumably from the SOTG, seeking to kill a man called Mullah Baz Mohammed burst into a house and gunned down six members of an unrelated family. In another incident, bad information led the SOTG in September to apparently kill a man named Rozi Khan, who subsequently turned out to be the district governor and close ally of Hamid Karzai.

Predictably, false identifications had been very much a part of the Phoenix story also. Vincent Okamoto, a lieutenant with the Phoenix program explained:

"The normal procedure would be to go into a village and just grab someone and say, ‘Where’s Nguyen so-and-so?’ Half the time the people were so afraid they would say anything. Then a Phoenix team would take the informant, put a sandbag over his head, poke out two holes so he could see, put commo wire around his neck like a long leash, and walk him through the village and say, ‘When we go by Nguyen’s house scratch your head.’ Then that night Phoenix would come back, knock on the door, and say, ‘April Fool, motherf**ker.’ Whoever answered the door would get wasted."

Rozi Khan’s death was not of that order. But consider the response of Defence Minister Joel Fitzgibbon, who subsequently told reporters that the death of any civilian was a setback in the battle for Afghan hearts and minds. The Age‘s Tom Hyland described Khan as "a warrior, former police chief, hereditary tribal leader and elected district governor" — but because Khan supported Hamid Karzai, Fitzgibbon labelled him a "civilian". By contrast, Dodd’s article describes another SOTG target Mullah Abdul Bari as "a former Taliban governor of Helmand province". If Khan was a civilian then presumably Abdul Bari was too — but Dodd accepts without comment the legitimacy of the SOTG killing him.

Again, the ambiguity is inherent in the concept of Taliban "infrastructure", a particularly nebulous notion in an Afghan context in which most civilians own automatic weapons and the insurgency entwines religion and military struggle. Would — for instance — a mullah who preached in favour of the Taliban be considered a civilian? Or would he be considered part of the Taliban infrastructure and thus fair game for assassination?

Its planners intended Phoenix as a "rifle shot" rather than "shotgun" approach, narrowly focussed against Vietcong leaders. But the program disrupted the Vietcong in the way that Truong Nhu Tang described partly because it also relied on what was known as Counter Terror (CT). The SEAL Elton Manzione touched upon the point in his description of how his PRU operated:

"We wrapped [detonator]cord around [prisoners’] necks and wired them to the detonator box. And basically what it did was blow their heads off [… the] general idea was to waste the first two. They planned the snatches that way. Pick up this guy because we’re pretty sure he’s VC cadre — these other guys just run errands for him. Or maybe they’re nobody; Tran, the farmer and his brother Nguyen. But bring in two. Put them in a row. By the time you get to your man he’s talking so fast you got to pop the weasel just to shut him up. I guess you could say that we wrote the book on terror."

Brutalities of that order were not about obtaining confessions so much as a method of spreading fear throughout entire communities that might otherwise have turned to the Vietcong. Wayne Cooper, a former Phoenix adviser, described how "CIA representatives recruited, organised, supplied and directly paid CT teams, whose function was to use Viet Cong techniques of terror — assassination, abuses, kidnappings and intimidation — against the Vietcong leadership". The Provincial Reconnaissance Units employed hardened criminals recruited from South Vietnamese jails with the promise of remissions proportionate to the number of communists they killed.

By 1970, as Paul Ham notes in his Vietnam: The Australian War, Phoenix had degenerated into "squads of wild-eyed, often drugged, Vietnamese killers roam[ing]the countryside and indiscriminately round[ing]up and tortur[ing]suspects or civilian sympathisers".

Again, there’s no evidence yet of anything similar taking place in Afghanistan. But it should not be forgotten that Phoenix, like the Vietnam War itself, is fundamentally a story of escalation. Special forces soldiers carrying out assassinations are — almost by definition — outside normal accountability, which creates the conditions for both atrocities and for cover-ups.

Thus Tom Hyland reports that when SAS soldiers accidentally shot a car full of civilians near Tarin Kowt in southern Afghanistan in early July 2006 they neither assisted the injured nor acknowledged their involvement, presumably confident that the rest of the world would never know.

It’s depressing to even have to argue these things. The conflict in Afghanistan was sold to the Australian public as a war of liberation. But here we are, seven years later, engaged in a strategy that traces its lineage to the darkest deeds of the Vietnam War.