The announcement by East Timor’s prime minister, Xanana Gusmao, that his country will begin military to military links with Indonesia has caused widespread surprise, given the deeply troubled history between the small, recently independent state and its large and previously belligerent neighbour. There are several benefits to this new arrangement, which will also see police-to-police links established. But there are also many unresolved issues.

Indonesia’s invasion of East Timor in 1975 led to the deaths of more than a quarter of its population, almost 200,000 people, with its final farewell being the destruction of most of the country and the murder of about 1500 more civilians. According to  Gusmao, it is now time to forgive and forget.

Having led East Timor’s resistance movement for much of the Indonesian occupation and being jailed by Indonesia, Gusmao is as familiar as anyone with Indonesia’s depredations during this time. He is also aware that effectively no one has ever been held to account for what the United Nations describes as war crimes and crimes against humanity in East Timor.

But, as the country’s leader, he knows that East Timor must learn to live cheek by jowl with its neighbour, even if that is sometimes difficult to swallow. He also knows that military links are an important part of positive international relations, helping to secure bonds of trust and co-operation.

Closer engagement with Indonesia also helps lessen East Timor’s reliance on Australia and other donor states, as part of its policy of spreading its friendship networks. China has already become an important contributor to East Timor broadening its relationships.

Many, too, in Australia’s security establishment, also want to see closer links with Indonesia. East Timor’s own closeness helps form part of a trilateral bond.

Yet despite the arguments in favour of closer ties to Indonesia’s military and police, problems persist. Apart from Indonesia’s security forces not being held accountable for crimes in East Timor, their more general culture of impunity for human rights abuses stands as a poor lesson for East Timor’s own security forces.

There have long been calls for extensive reform of East Timor’s security sector yet, apart from some semi-useful training, to date, little has been done. Despite its history of fighting Indonesia, East Timor’s small army takes many of its cues from the Indonesian army, not least its penchant for involvement in civilian affairs and its desire to control the police, which even Indonesia gave up over a decade ago.

East Timor’s police, too, were largely drawn from those worked as police under Indonesia and continue to have a reputation for brutality and corruption. The emulation of Indonesia’s security forces by those in East Timor is disturbing, not least to its citizens who have long wanted a clean and accountable security apparatus that protects, not intimidates, them.

While Indonesia’s own security sector has undergone significant change over the past decade, numerous reports and analyses continue to show that it is engaged in private business and corrupt or criminal practices and that its reform process has effectively stopped. This is a less than ideal role model for East Timor’s own security forces.

As with other overtures by the East Timorese government to Indonesia, the overwhelming response of East Timorese people to this announcement is likely to be one of dismay. There is, then, something of a disconnect between East Timor as a state and between East Timor as a nation of people.

Having a disconnect between the state and its citizens is all too common in developing countries and is a frequent cause of internal conflict, of which recent events in the south-west show East Timor continuing to be vulnerable. Many people, not least in East Timor itself, had hoped their state might be more cognisant of their needs and aspirations.

Perhaps, then, the balancing act of East Timor’s external needs and those of its people will sometimes tip in favour of real politik over justice, as it has done to date. But there might also be a point where engagement should extend only to the point of meeting practical needs rather than comforting military leaders, to being more nuanced and subtle rather than absolute and complete, and where co-operation is not unconditional but recognises that much ground still needs to be covered before alliances can be said to be of common interest.

East Timor may have jumped a little more quickly and a little further than was absolutely desirable, no doubt prompted by its very real awareness of its size and proximity to its nearest neighbour. As Australia re-assesses its own regional relations with a view to even closer ties, it might also want to consider the extent to which conditions might apply to such further engagement.

*Professor Damien Kingsbury is director of the Centre for Citizenship, Development and Human Rights at Deakin University