Indonesia's outgoing parliament is preparing for an historic send-off. Democratic reforms which began with the overthrow of the authoritarian former President Soeharto in 1998 set a timetable for the gradual abolition of reserved parliamentary seats for the armed forces.

On October 1 a new elected legislature is due to be sworn in. For the first time in more than four decades there won't be a military uniform in sight.

The process of sending Indonesia's soldiers back to the barracks – and formally subjugating the armed forces to the authority of a democratically elected civilian government – will finally be complete. This is an important milestone for Indonesia's young democracy.

Australia and other Western nations have long been troubled by the politicisation of Indonesia's military and the abusive way power has too often been wielded.

The transition suggests a welcome easing of bilateral tensions. However, a series of recent judgements in Indonesia's courts has shifted attention to another aspect of the military's power: its ability to pull strings through less formal channels.

This month an appeals court overturned the convictions of all remaining officers charged over human rights abuses during the Indonesian military occupation of East Timor. Another tribunal cleared the commander of the notorious special forces, Kopassus, over a massacre of protesters more than 20 years ago. Not a single member of Indonesia's security forces has been jailed for crimes against humanity, despite the well-documented atrocities of the Soeharto era and new abuses since.

The failure to secure even a symbolic human rights conviction sends a troubling signal; that the military can operate with impunity. A recent ruling by the Constitutional Court established a legal impediment to retrospective justice.

However, the human rights prosecutions against senior Indonesian officers did not fail on this legal technicality. They failed because of the wavering resolve of civilian politicians. In the lead up to September's presidential run-off, political alliances are fluid, and deal making rife. There is no doubt the armed forces still represent a formidable national network and, as such, retain much leverage behind the scenes.

The Indonesian military is engaged in two protracted security operations against separatist groups. Jakarta considered the loss of East Timor in 1999 an international humiliation. It is now determined to crush independence movements in Aceh and Papua and, in doing so, to retain control of the provinces' considerable natural resources. This increasing militarisation mirrors the costly, but ultimately unsuccessful, Soeharto-era strategy of employing overwhelming force. Indonesia's own human rights commission last week concluded troops had recently committed gross abuses in several Papuan towns.

Australia assisted East Timor's transition to independence, but Canberra does not support independence movements elsewhere. This should not mean Canberra cannot press Jakarta on human rights or the underlying economic inequities which will only continue to stoke the conflicts in Aceh and Papua.

Successful national elections earlier this year consolidated Indonesia's democratic reforms. Respect for human rights and the rule of law, however, are equally important pillars of any credible democracy.