The East Timorese Government was handed a heaven-sent opportunity this week to begin the long overdue process of healing the rifts so vividly exposed by last May's wave of violence.

But to the dismay of many, Prime Minister Jose Ramos-Horta, appears to have put loyalty to the military ahead of the long-term interests of East Timor, and with it the possibility that the yawning gulf between the ordinary people and the governing elites can be bridged.

A United Nations Special Commission of Inquiry – established at the direct invitation of Ramos-Horta when he was still senior minister and minister for foreign affairs – delivered its report on Tuesday, with one of its findings being that the chief of the country's armed forces, Brigadier-General Taur Matan Ruak, be prosecuted for his role in the violence that killed more than 30 people and displaced more than 150,000 people from their homes in Dili.

Also recommended for prosecution were former interior minister Rogerio Lobato, renegade army major Alfredo Reinado and umpteen other rebel soldiers, civilians and security force members suspected of direct involvement in the violence. Shortly after the report was issued, however, Ramos-Horta issued a public statement saying he had full confidence in Ruak and his leadership. He went further, saying that "Throughout the crisis, the senior command of F-FDTL [East Timor's defence force] showed zeal and discipline."

Ramos-Horta's defence of Ruak, while disappointing, is not surprising insofar as the defence force, for historical reasons, plays a substantial, even pivotal, role in East Timorese politics. But what is extraordinary is that Ramos-Horta, who has largely appeared be above the factional cronyism that characterised the administration of his predecessor, Mari Alkatiri, should now be implicating himself in the worst aspects of an incestuous political culture that has brought Asia's smallest and poorest nation to its knees barely four years after its independence.

The UN commission is well aware of the fragility of East Timor's state institutions and the weakness of the rule of law. This might explain why it chose to reserve judgment on the role of Alkatiri. Instead, it called for further investigations by Timorese authorities to determine whether the former prime minister should face criminal charges over the transfer of defence force weapons to civilians who used them to commit assorted crimes and violations of human rights during the worst days of the crisis.

Whether the country's legal system is sufficiently independent to investigate one of the country's most powerful politicians remains unclear. Certainly, the Parliament, which is dominated by the powerful Fretilin faction (and the one which Alkatiri controls), seems unwilling to take a leading role, with the head of the faction, Elizario Fereira, saying on Wednesday that legal action should be left to the judiciary.

As for the role of President Xanana Gusmao during the troubles – during which time he appeared to remain largely above the fray – the UN commission cleared him of allegations that he'd ordered Reinado "to carry out criminal actions" but he was criticised for his failure to show "more restraint and respect for institutional channels in communicating directly with Reinado after his desertion".

Under the constitution, Gusmao's ability to directly shape future events in East Timor as president is limited – his response to the report was to call on the Parliament to "quickly take political and legislative or legal actions". Fereira's comment showed this is likely to be a forlorn hope because the country's judiciary, like East Timor's other institutions, simply has not had the time to develop the robustness of the legal systems associated with democracies that carefully observe the doctrine of the separation of powers.

East Timor's inability to abandon the most corrosive aspects of its colonial heritage, as well as the legacy of the armed struggle for independence that led to the creation of an expensive and unnecessary army and which simply exacerbated political and ethnic rivalries, are at the heart of its malaise, and only the country's elites can rectify them.

Earlier this month, the International Crisis Group issued a report on East Timor, in which it iterated the need for reforms in the security sector before the country's political crisis could begin to be resolved. But the authors were insistent on the need for "enormous political magnanimity on the part of a few key actors".

The recommendations of the UN represent an ideal means of strengthening East Timor's fragile foundations: "Justice, peace and democracy are mutually reinforcing imperatives. If peace and democracy are to be advanced, justice must be effective and visible."

That the country leaders seem, at this early stage anyway, to be reluctant to embrace hard truths, is regrettable. The East Timorese themselves, who were promised so much at the time of independence, have every right to feel aggrieved.