Sian Powell, Jakarta – Two Supreme Court judges have risked high-level political opprobrium by criticising Indonesian armed forces' crimes in East Timor in 1999.

In only the court's third dissenting opinion, the two judges ruled against Indonesia's ad hoc tribunal on East Timor, finding five senior army and police officers guilty of gross human rights abuses.

Supreme Court judge Artidjo Alkostar told The Weekend Australian that in terms of human rights law, the five officers were guilty of acts of omission. He said that although they were aware of militia attacks on independence supporters sheltering in a church in the East Timorese town of Suai in September, 1999, they failed to protect the victims. "They knew there was killing in the church," he said. "They were outside the church."

Military abuses in East Timor have been a politically sensitive issue for decades, and international condemnation accelerated after the carnage in 1999, when East Timor chose independence from Indonesia.

As expected, the other three Supreme Court judges on the case found the officers innocent in a decision released on March 3, allowing the men to avoid penalty. The judges upheld the rulings of Indonesia's East Timor tribunal, which has been condemned as a whitewash. It has acquitted most of the 18 officers and civil servants it called for trial, and handed down extremely light sentences for the rest.

The four senior Indonesian soldiers and a senior police officer implicated in the Suai church massacre – and found guilty by Judge Alkostar and his colleague, Sumaryo Suryokusumo – earlier were acquitted by the tribunal. Armed militias killed at least 27 people in the Suai slaughter, including three Catholic priests. In his judgment, Judge Alkostar ruled that all five officers – two army colonels, two army majors and an adjutant police commissioner – deserved jail terms of between 10 years and 10 1/2 years.

"What happened in the Suai church on September 6 1999 was a crime against humanity," Judge Alkostar wrote. "The attack on 27 civilians was part of the broadly based and systematic attack which happened in East Timor."

The question of Indonesian military abuses in East Timor surfaced this week when UN-funded Serious Crimes Unit prosecutors released a damning summary of evidence and legal argument in the case against Wiranto, the Indonesian armed forces commander during 1999. The summary declared Wiranto guilty of chain-of-command responsibility. "Militias were formed, funded, armed and controlled by the Indonesian army with the knowledge of the accused," the summary said.

However, Indonesia's East Timor tribunal failed to even call Wiranto. Judge Alkostar said his judgment did not relate to chain-of-command, but direct responsibility. He did not rule out acts of commission by soldiers, as well as acts of omission.

"The explanations of the witnesses declared that besides those from the groups of Laksaur and Mahidi (militias), there were also members of the Indonesian army from Kodim 1635 and the police force involved in the attack on refugees in the church complex," the judge wrote.

The Supreme Court cleared Golkar party leader Akbar Tandjung last month of embezzlement, provoking a hailstorm of criticism. One dissenting judge in that case said the parliament speaker was guilty of diverting 40 billion rupiah ($8 million at the time) intended for the poor.

The court also this month unanimously halved the sentence of the terrorist-linked Islamic preacher Abu Bakar Bashir to 18 months. He is now scheduled to be released from prison on April 30.