Australia’s precise role in bringing independence to Timor-Leste two decades ago continues to simmer as unsettled business at the heart of modern Australian diplomatic and military history.

Twenty years is the blink of an eye, of course. And my memories of having a front-row seat on the Australian domestic politics, and the diplomatic and military movements preceding and following the East Timorese autonomy ballot, are vivid.

John Howard later pointed to two key moments of his prime ministership about which he is most proud: his government’s response to the 1996 Port Arthur massacre and Australia’s part in East Timor.

East Timor: Indonesia's invasion and the long road to independence Read more

After the violence diminished, and as the fledgling nation began to govern itself (and even as our spies bugged Dili’s cabinet room to gain unfair advantage in minerals negotiations) Australia has cast itself as the hero of East Timor. The Australian-led Interfet force, ably headed by a later governor general, Peter Cosgrove, showed East Timor – in stark contrast to the morally (and otherwise) venal Indonesia military (TNI), with its orchestration of the pro-integration militias in the province – what a disciplined military force looked like.

But the truth was that throughout 1999, as tensions steadily rose in East Timor after Indonesia’s president BJ Habibie (effectively a puppet of the military) announced an act of self-determination, Australia had been anxious to avoid any military peacekeeping deployment and eager to appease Jakarta by downplaying formal, though undeniable, links between TNI and the militias.

A raft of declassified US cables and other documents released by the US-based Indonesia and East Timor project further illuminates what the subversive (and in my view, correct) analysis of the times has always shown. And that is: our federal government was eager to downplay its real differences with the US throughout 1999 on the need for an early peacekeeping deployment to end the anticipated and eventual violence, yet it also ultimately relied on the threat of American military muscle to get Jakarta to allow the UN-mandated Interfet into East Timor.

Play Video 4:13 East Timor independence: a short history of a long and brutal struggle – video

Something else the cables make unambiguous: Australian ministers, including Howard and the then foreign minister, Alexander Downer, dismissed suggestions TNI was carefully orchestrating the violence by asserting that only “wild elements” or “rogue elements” were involved, but the US Defence Intelligence Agency was making those connections unambiguous.

Australia would have seen much of the same intelligence.

Such were the lengths Australia was going to help Jakarta save face – to protect its precious bilateral relationship with Indonesia.

The documents also highlight the realpolitik behind Washington’s attempts to preserve military relations with Indonesia, despite its detailed knowledge of the TNI-orchestrated violence and human rights concerns in Congress.

“Militia members in east Timor have had unrestricted access to the Indonesian military arsenal, acquiring small arms and hand grenades as supplements to traditional weapons such as machetes and spears,” reads one assessment of the militias, who killed “thousands”.

As a Canberra-based foreign affairs and defence correspondent, on 1 August 1999 I reported for the Sunday Age how Australian officials had earlier that year talked down US overtures for an early peacekeeping mission (to avoid the violence that eventually transpired), possibly involving Marines.

Downer was outraged. He issued multiple denials about the US discussion of a Marine deployment or of any difference in approach between Australia and Washington.

Nine days later I published in the Age the secret Australian cable detailing the meeting between Australian and US officials in which stark differences of potential approach and strategy were highlighted. America had raised the prospect of sending 15,000 US troops into East Timor via Darwin.

Late that evening Downer went into the House of Representatives to admit he had not read the secret Australian cable about the US contingency on troops – the same cable in which a key “area of difference” in approach between the US and Australia was spelt out.

Downer had sought, in both Australia and the US, to belittle the first article and to challenge the credibility of its authorship. The lengths he went to are made plain in one of the newly released cables by the Indonesia and East Timor project.

As pre-ballot tensions were rising in East Timor, US cabling on 2 August 1999 makes it clear that a priority in Canberra for the Australian foreign minister was managing the embarrassment of any suggestion of a US-Australia rift on peacekeeping or anything else.

A department of Foreign Affairs and Trade deputy secretary, Neil Mules, told the US embassy in Canberra that the articles “infuriated FM Downer”.

“Downer strongly denied their veracity in an August 1 television interview [the day the Sunday Age published the most contentious article] and ordered DFAT to send to the Australian Embassy in Washington for transmission to the Department press points he is using to rebut the articles ... Mules urged that, in responding to press queries about these stories, USG [United States Government] spokesmen make similar points.”

International PR while the militias prepared to torch Dili!

In his 2004 book, Reluctant Saviour, Clinton Fernandes, a historian and former Australian military intelligence officer who was intimate with the East Timor military operation, wrote: “The problem was that for the whole of 1999, the government had lobbied to keep peacekeepers out [of East Timor]. It now [by August 1999] worked frantically to allow international forces to enter East Timor in order to prevent a political crisis in Australia. Contrary to Howard and Downer’s earlier claims, repeated even today when asked why peacekeepers weren’t sent in before the ballot, four days of diplomatic pressure is all it took for Indonesia to agree to foreign troops.”

The critically effective “diplomatic” pressure (which I read, in the light of these now released cables, to be more tantamount to implied US military threat) comes not from Australia, however, but from the US military establishment.

The newly released cables make apparent how the US State Department, always carefully managing Washington’s bilateral relations with Jakarta, played a secondary role to US Defense in the critical days before Habibie agreed to allow Interfet into East Timor.

While the then Indonesian foreign minister, Ali Alatas, echoing other similarly threatening voices in the Jakarta administration, warned that “nations willing to send peacekeepers to the province would have to shoot their way in”, the US military establishment was figuratively reading the riot act to Indonesian military chief Wiranto.

East Timor descended into extreme violence after the 4 September 1999 ballot result, which overwhelmingly favoured independence. The Indonesian military, responsible for security, declared martial law on 6 September, while also aiding the militias. The international community was outraged but needed Indonesian permission before a UN-sanctioned force would be allowed in.

The military controlled Habibie. So, plainly, the Indonesian military had to be convinced – perhaps in the only way it understood, with the implied threat of heavy consequence – to capitulate.

On 8 September the commander of US forces in the Pacific, Dennis Blair, met Wiranto.

He told Wiranto if East Timor’s security continued to deteriorate “it will do potentially irrevocable damage to Indonesia’s relationship with the rest of the world, including the US”. According to the US cable recording the meeting, Blair left his talking points with Wiranto.

'Infuriated' Alexander Downer tried to get US officials to mask Australian inaction on East Timor Read more

Point five reads: “The whole world is watching as this tragedy unfolds, and international condemnation of Indonesia has grown to a fever pitch. The window of opportunity in which Indonesia can salvage its relations with the world is rapidly shutting ... I appeal to you to let the international community help Indonesia help itself.”

The biggest military gorilla in the South Pacific had beaten its chest.

On 12 September Habibie, after a cabinet meeting including Wiranto, announced that Indonesia would accept peacekeepers. Interfet deployed eight days later.

The release of these US cables sheds more light on Australia’s true, not always heroic, part in the liberation of East Timor. Just as they will fuel more argument about the history of that combative political, diplomatic, military – and journalistic – time.

• Paul Daley is a Guardian Australia columnist