The article presents the spying scandal as simply the latest instance of "constant foreign intervention in Indonesian affairs that few Australians are aware of".
Professor Reuter, an anthropologist and an Australian Research Council Future Fellow, suggests that Australia owes Indonesia an apology for its part in the post-war attempt by the Allies to help the Dutch return as imperial masters after the defeat of the Japanese.
"The British have since apologized for this cruel attempt to stifle the young nation's struggle for freedom and sovereignty. Australia has not," he writes.
Professor Reid, an expert on the history of Southeast Asia, said "a more balanced and self-critical remembrance of past wars in which Australia has participated would certainly be welcome.
"But Australia's role in the restoration of colonial rule in eastern Indonesia in 1945-6 seems an unlikely place to start.
"The whole Pacific War was fought to defend a creaky colonial system, and in its latter stages racially-tinged atrocities were frequently committed against Japanese who were wounded or attempted to surrender.
"The destruction of Borneo cities in 1945, particularly Balikpapan, was on a massive scale.
"As against this pattern, the Australian repression of the modest stirrings of the independence movement in eastern Indonesia in 1945-6 was not notably bloody - though there were indeed casualties.
"More remarkable in the context of the time was how many diggers, especially those connected with the Communist Party, were prepared to support independence actively.
"One of the reasons the Indonesian quasi-Parliament gave for thanking Australia in November 1945 for its support was that Australian soldiers in Borneo were reported to have supported independence demonstrations."
In his article, Professor Reuter does not mention Australia's early shift to diplomatic support for Indonesian independence.
He also charges Australia with having applauded as the Suharto military regime presided over "one of the greatest genocides of the 20th century" in 1965-66.
"Up to one million innocent Indonesian civilians were butchered over the following year at a rate of 1,500 people per day, to the applause of western powers including Australia," he writes.
"The pretext (for Suharto's seizure of power) was a fake coup attempt, falsely attributed to the Indonesian Communist Party (PKI).
"The deep involvement of British and American intelligence in staging this bloody military coup, similar to the Pinochet takeover of Chile, is beyond reasonable doubt."
An expert on the period, Robert Cribb of the Australian National University, said this account of the 1965 events was "seriously flawed".
"It is now certain that the PKI leader, DN Aidit, was involved in the coup that triggered the army crackdown and the massacres," Professor Cribb said.
"To call the army's action a pre-emptive coup is simply wrong. It is also wrong to call the 30th of September Movement a 'fake coup'.
"It may have had limited aims, but the limited aims still involved a decisive shift to the Left - the plotters seized power in the name of a Revolutionary Council."
As for the mass killings, Professor Cribb said the "safest estimate" of the number killed was half a million.
The Reuter article was first criticised by Adrian Vickers, professor of Southeast Asian studies at the University of Sydney.
He seized upon Professor Reuter's claim that during the independence struggle "Australian troops participated in the occupation of the outer islands, including Bali, and were involved in massacres".
Professor Vickers said it was simply not true that Australian troops had occupied Bali during the early period in which Allied forces were seeking to hold positions for the returning Dutch.
And he said he had never heard of any evidence of Australian troops being implicated in atrocities against Indonesian independence fighters.
There were Australian troops, his father included, stationed in what became eastern Indonesia.
"Some volunteered to go to Ambon for the post-war occupation. Dad said it was dead boring, the only action was fishing with dynamite in Ambon Harbour," he said.
After Professor Vickers complained, The Conversation edited the Reuter article, withdrawing the claim that Australian troops had occupied Bali and taken part in massacres. These claims remain unchanged on the Jakarta Post website.
In the debate that ensued, Professor Reuter acknowledged the passage was "poorly worded," and said he had relied on "a senior Indonesian official" as his source.
He suggested Australia could be held responsible in a more general way for the unequal fight between poorly equipped Indonesian militants and the Allied forces of which Australia was part.
"Everyone supporting the reoccupation was at least indirectly 'involved' because the stated aim thereof was to create military security for the return of the Dutch East Indies Government," he said.
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