In 2000, the then Indonesian president, Abdurrahman Wahid, performed one of the most difficult acts a nation's leader can perform. He apologised to the victims, both dead and maimed, of his country's violent actions.

Mr Wahid went to the Santa Cruz cemetery in East Timor where in 1991 dozens of people were massacred and said: "I would like to apologise for the things that have happened in the past. To the victims or the families of Santa Cruz and those friends who are buried in the military cemetery – these are the victims of circumstances we didn't want."

Although he was not leader in 1991, Mr Wahid accepted that as leader he had a responsibility for his country's past deeds. Two recent examples of this ethic have been the German Chancellor Angela Merkel addressing the Israeli Parliament in March of her country's "historic responsibility" to the victims of the Holocaust; the second was the apology of Canada's Prime Minister, Stephen Harper, to his country's indigenous population for past government policy. There was also, of course, Kevin Rudd's apology to the stolen generation.

Indonesia's responsibility for its actions, and its obligation to acknowledge them, have been brought into focus this past week with news of the report by the Commission of Truth and Friendship into the 1999 atrocities that occurred during the period of East Timor's vote for independence.

Yesterday in Bali, Indonesian President Susilo Bambang Yudhoyono and East Timorese President Jose Ramos Horta officially accepted the report. However, in doing so, Yudhoyono only expressed regret at his country's involvement. An apology was not mentioned. This is not good enough. It is an elemental link in the chain that to accept responsibility for an act of violence carries with it the duty to say sorry for that action. In this case, there were many acts and they were of the most heinous kind.

The commission's report details a co-ordinated campaign by Indonesia of violence, including massacre, rape and torture, against Timorese civilians. It is estimated that about 1500 died.

The Indonesian Government's stance was foreshadowed on Monday when Defence Minister Juwono Sudarsono said: "There will be no apology; it is only about remorse, which is deep regret by both parties, from both governments, both presidents for their people."

Given that the report recommends an apology, this attitude is regrettable. Indonesia has indicated it recognises its "moral obligation", yet it seems that obligation only goes so far. Expressing remorse does not bring closure in the same way or with the same commitment that an apology does.

The East Timorese in 1999 were witnesses to one of the historic moments of a people: the birth of a nation. It was to be their fate that its creation came through violent opposition. The report released yesterday, and which the The Age reported exclusively last Saturday, found that Indonesia's police, army and civilian government officials provided funds, armed and co-ordinated militias opposed to independence. Indonesia bore "institutional responsibility" for the deaths of up to 1500 people, and the rape, torture, illegal detention and deportations. The report, which was commissioned by both governments to try to thwart a UN investigation into the events of 1999, did find that both sides committed offences, but that Indonesia was the prime agent of the violence.

Recognising those responsible, and apologising, however, is only one side of the coin. The other is bringing the perpetrators of the violence to justice. It is here that a resolution of the past faces a troubled future. The report concedes that its findings have "no judicial or quasi-judicial powers". In other words, it cannot compel prosecutions despite finding that crimes against humanity had occurred. In fact, not one person is serving time in jail for any offence that occurred in 1999. In April this year, Eurico Guterres, a militia leader, was freed from jail after his conviction was overturned.

Dr Yudhoyono does himself no services by trying to play down his country's role in the human rights abuses. In 1999, he was a general based in Jakarta, and was reported to have said at the time that he was worried international opinion might view events in East Timor as a "great human tragedy... when in reality it is not". Australia has also done itself no services in the past by trading speaking out against abuses for good relations with Jakarta.

The findings of the Truth and Friendship Commission clearly have shown Dr Yudhoyono's perceptions of reality to be false. The 1500 victims of 1999 cannot speak for themselves. It behoves the leader of the state that led to their deaths to speak to them, and to say sorry.