Shawn Donnan – Under the Suharto regime, Toga Tambunan spent 13 years detained without trial in an assortment of jails and prison camps. He was beaten for reasons such as planting flowers that unexpectedly bloomed a communist red. When he was finally released in 1978 he was shunned by a father-in-law ashamed of his past as a political prisoner.

So, more than seven years after Suharto's 1998 fall, the former poet and journalist believes he has a right to be compensated for his suffering. Or at least to have it formally recognised in the hope that future generations of Indonesians might avoid the same fate.

"I have already forgiven the people who tortured me and who beat me. Even Suharto I have forgiven," he says. "But I want to make sure the system will be changed so they can't do the same thing again." It has been 40 years since the September 30 1965 coup that led to Suharto's 32-year rule, and Indonesia these days does a commendable job of asserting its place as the world's third largest democracy.

For victims of Indonesia's bloody crackdown on alleged communists and their sympathisers, however, justice has been slow. Historians and leading Indonesians say this is just one of the legacies of history.

From small villages in Borneo, Java and Sumatra to the holiday island of Bali, between 500,000 and 2m people were killed in the military-led crackdown that followed the coup. Historians estimate 1m more were thrown in jail, many for more than a decade.

But what happened in 1965 is discussed in public only rarely in Indonesia. Left mostly unchallenged is the official version of events, as endorsed by Suharto that the Indonesian Communist party, or PKI, was behind the attempted coup and the future strongman heroically helped save south-east Asia's largest economy from the ravages of Marxism.

"It is the biggest and saddest tragedy that we have ever had," says Taufik Abdullah, a historian at the Indonesian Institute of Sciences. "But in Indonesia many people prefer to forget." That is aided by a decidedly murky history. In 2003, Mr Abdullah was asked to lead a team to draft a definitive history of the September 30 coup. Two years on he and his team have managed, he says, to narrow it down to half-a-dozen possible scenarios and given up narrowing it any further.

Even that exercise has proved controversial. Under pressure from radical Islamic groups, the government earlier this year abandoned a plan to amend the official high school history curriculum to reflect alternative versions of who might have been behind the 1965 coup. (Among the favourites: that Suharto himself plotted the coup in a convoluted effort to seize power or that the CIA backed it to bring about the demise of an increasingly influential PKI.) Indonesia's parliament last year called for a truth and reconciliation commission modelled on South Africa's to resolve Suharto-era atrocities.

But this remains only an idea debated at symposiums for now. Who would sit on the commission is unclear, as is the history it would be allowed to explore.

Part of the issue, say historians and activists, is that many in Indonesia's political elite owe their stations to the 84-year-old Suharto, who has repeatedly avoided trial in spite of allegations that he and his family stole as much as $35bn during his rule.

Though he is considered a reformist figure by many, President Susilo Bambang Yudhoyono is a former Suharto-era general. Mr Yudhoyono's father-in-law, Sarwo Edhy, was the general who led the 1965 crackdown on suspected communists.

Indonesia's constitutional court last year restored the right of former political prisoners and their families to run for elected office. Recent governments have eliminated the special identity cards they were once required to carry.

Bans on relatives of accused communists being hired as civil servants are also supposed to have been lifted, though it remains unclear if this is carried out in practice.

But efforts to secure compensation for former political prisoners and other victims have gone nowhere.

A Jakarta court earlier this month dismissed a class action lawsuit filed by a group of 1965 victims against Suharto, Mr Yudhoyono and three other presidents. Lawyers for the victims have filed an appeal.

[Additional reporting by Taufan Hidayat.]