Don Greenlees, Jakarta – Shortly after dawn on April 7, 1999, independence, let alone justice, for the East Timorese seemed a distant dream in the fearful and empty streets of Liquica.

The population, which had fallen victim the day before to the worst in a long history of violent acts, had either fled to the hills or were hiding in their homes. Liquica belonged to the militia, the army and the police.

In the patchwork of bloodstains in the yard of the Ave Maria church, 200m down a slope towards the sea from the local military command and the mayor's office, were the telltale signs of a massacre.

East Timor's Catholic Bishop Carlos Belo estimated then that at least 25 people had died. United Nations investigators later put the death toll at almost 60. The victims were simple people – farmers, fishermen and local traders, most of whom supported East Timorese independence from Indonesia.

As for the perpetrators, that was no secret. The military-backed Besi Merah Putih (Red and White Iron) militia wandered through the streets bearing their usual collection of machetes and homemade guns. They casually mingled and joked with soldiers, reclined in the shade of a tree outside the police headquarters and wandered through the grounds of the office of the mayor, Leoneto Martins.

The few locals who still ventured on to the streets trembled with fear as they spoke. Still in shock, they could give only garbled accounts of what had happened. Months later, Liquica defied the sustained intimidation and violence, and like other districts of East Timor, voted overwhelmingly to separate from Indonesia. The victory came at great cost – 80 per cent of the town was burned out by the retreating Indonesian loyalists.

But out of this tragedy came the hope that, just like in Bosnia and Rwanda, the lofty ideals spoken about by UN officials would one day translate into justice.

In a central Jakarta courtroom on Friday afternoon, the people of Liquica received their answer. A panel of five judges from Indonesia's Human Rights Court dismissed all charges against Liquica's army commander Lieutenant Colonel Asep Kuswandi, its police chief, Lieutenant Colonel Adios Salova and Mr Martins.

"It is true there have been human rights abuses but they were carried out by the Red and White Iron group, which has no relation with the defendants," chief judge Sutiarso said.

The ruling confirmed a pattern. Of 12 defendants tried for crimes in East Timor, only two have been convicted. Both were ethnic East Timorese, now free while appealing their sentences. Every soldier or policeman brought before the court has been acquitted.

The court's performance lends credence to claims it is abiding by a deal struck between the Government and the armed forces that no member of the security forces would be convicted.

The aversion to convicting soldiers or police has been in no case more obvious than the April 6 Liquica massacre. While Judge Sutiarso said there was no connection between the militia, the mayor, police and army commanders, an Indonesian police officer who investigated shortly after the massacre had a different view.

Major Carlo Tewu wrote: "Witnesses saw the attackers were the Red and White Iron group and members of the Kodim (district army headquarters) who at the time were wearing plain civilian clothes." The court seems not to have found the report of a senior police officer relevant.

Local parish priest Father Rafael dos Santos reported seeing militia commanders mixing with the defendants when he was taken to military headquarters just after the attack started. His evidence did not count either.

An Australian embassy report, based on its own investigation, found "evidence that ABRI [the Indonesian armed forces] assisted Besi Merah Putih to take control of Liquica, creating a situation which led to the violence on April 6". "Militia personnel appeared to be in close contact with and gathering at the military district headquarters" in the days after the massacre, the report said.

Human rights groups say they have now given up any hope of justice coming from the Human Rights Courts in Indonesia.

[Don Greenlees was among the first journalists into Liquica after the massacre.]