Damon Kingsbury – Defence Minister Senator Robert Hill has said that in a bid to counter terrorism, Australia will restore its links with the Indonesian army's special forces, Kopassus, and strengthen intelligence links with the country.

This decision was disturbingly predictable and very short-sighted.

The government has been edging towards closer cooperation with the Indonesian military for over a year but has been restrained by the popular memory of why military links were broken off.

The public perception of events in East Timor in 1999 has not appreciably changed but the government now sees terrorism, in particular that with a radical Islamic character, as being the prime threat.

However, support for the military generally, and Kopassus in particular, is a major error of judgement at two levels.

The first is the history of Kopassus' involvement with terrorism, along with the TNI more generally. The second is that such support implicitly endorses and reinforces the types of political structures that have led to most of Indonesia's problems now.

The Kopassus role in training and leading East Timor's militias is well documented, but what is less clearly recorded is this same role with other shadowy militia groups in places like West Papua, Maluku (Ambon) and Aceh. In each case, Kopassus has trained armed vigilante groups to deflect from the military responsibility for atrocities.

Kopassus members were, for example, involved in the training of the notorious Laskar Jihad in West Java. This group was responsible for the deaths of many thousands in Maluku and Central Sulawesi and many members had previously fought with the Taliban and Al Qaeda in Afghanistan.

The organisation most publicly linked with the Bali bombing, Jemaah Islamiyah, was also one of the sources of funds for the Laskar Jihad. It was just a short step from Jemaah Islamiyah to Kopassus, especially via the Green (Islamic) generals of the Soeharto era.

Kopassus also had its modus operandi stamped all over the murders of hundreds of moderate Islamic clerics in East Java in late 1998 – the so-called Ninja murders. It was also involved in the kidnapping and murder of student activists in 1998, political activists, unionists and others throughout the New Order period and the killings in East Timor from 1975 until 1999.

It is Kopassus members who are charged with the murder of Papuan independence leader Theys Eluay in November 2001.

The TNI has also been implicated in the recent attack near the Freeport mine in West Papua, in which two American and an Indonesian were killed.

If there was any doubt about the formal – as opposed to rogue element – role of Kopassus, it was spelled out in its training manual. This cited tactics and techniques for conducting psychological warfare, propaganda, kidnapping, terror, agitation, sabotage and other operations. This is not directed against external enemies of the state, but against Indonesian citizens.

Kopassus does have some small claim to opposing terrorism. In the early 1980s a small radical Islamic group referred to by the military as Komando Jihad bombed the Borobudur Buddhist monument in Central Java and in 1981 hijacked a plane to Bangkok. Kopassus troops stormed the plane and rescued most of the passengers and aircrew. The Komando Jihad was in fact set up by Major-General Ali Murtopo to discredit political Islam ahead of the 1982 elections.

In terms of Australia's long-term relations with Indonesia, a foreign policy position that again backs the military will end up having a profoundly negative impact on civil and political rights in Indonesia.

We are already seeing the military taking a repressive line in West Papua and Aceh. The continued detention in Aceh of Australian-based academic Dr Lesley McCulloch on a visa charge is a small but meaningful illustration of that approach.

Interestingly, Politics and Security Minister Susilo Bambang Yudhoyono has already warned of more terror attacks, but specifically in Aceh. This meets the TNI's long-term plan of having the Free Aceh Movement listed as a terrorist group even though its independence claim is purely local.

Yudhoyono's comments on the terrorism that led to Bali, however, have been far more subdued and equivocal.

At a time when there was still some, albeit fading, hope of reducing the TNI's political role, this move will legitimise its claim to be the guardian of the state. The TNI will in any case use Bali to assert its authority and, as so often in the past, Indonesia is likely to see its fledgling middle ground consumed by extremism on either side.

In this, Australian foreign policy advice derives from a narrow source, one that saw Soeharto's corruption as not a problem, his East Timor militias as not dangerous and believed that there were no meaningful militia-TNI links.

It also posited recently that radical Islam in Indonesia did not have terror links. That same source of advice is now recommending that Australia back Kopassus.

How often do we need to get it wrong before we start getting it right?

Australia's policy must recognise Indonesia's problems that lead to resentment and attempt to address, rather than repress, them. Support for the judiciary, police investigators and the health and education sectors will do much more to address the real problems.

Support for the TNI, and in particular its most brutal branch, Kopassus, may eventually restore stability, of a brittle type. And it may not. But the price now being paid in the form of support for Indonesia's Islamist extremism is a consequence of political manipulation and repression under the previous military-dominated government.

Australia's support for another one would be a profound mistake.

[Damien Kingsbury is a senior lecturer, philosophical, political and international studies, Deakin University.]