It was 4am on Oct 1, 1965.

Brigadier-General Donald Izacus Panjaitan knew that the soldiers-turned-insurgents had come for him, but he was not going to be taken without a fight.

The rebels had set upon his two-storey house in Kebayoran Baru, South Jakarta, where he lived with his family.

"I woke up after hearing footsteps of people in boots... it turned out we had been surrounded by members of the military," said Ms Catherine, the eldest daughter of the late general, who was just 17 at the time.

"My father was waiting upstairs, he cocked his rifle but it jammed... so he didn't get a chance to defend himself before he was murdered."

Her father and six other generals were killed later that morning during the attempted coup, allegedly backed by communist elements in Indonesia.

STARTING THE HEALING PROCESS

Establishing the location of those mass graves is a first step towards identifying the victims buried within and the circumstances of their deaths.

MR PHELIM KINE from Human Rights Watch on President Joko's effort to begin the process of reconciliation for the government's 1965 crackdown.

• About the purge

• An attempted military coup, allegedly backed by communist elements in Indonesia, led to the anti-communist purge across the country between 1965 and 1966 with more than 500,000 deaths, according to estimates by human rights groups.

  Many were said to have been executed or jailed despite having weak links to the Reds.

  Estimates since then have ranged from fewer than 1,000 to as high as 3 million, The Jakarta Post reported last month.

The uprising was quickly crushed by troops loyal to General Suharto but it sparked an anti-communist purge across the country between 1965 and 1966.

The bloody massacre by local pro-government groups led to more than 500,000 deaths across the country, estimates human rights groups.

Many were said to have been indiscriminately executed or jailed despite having weak links to the Reds.

Ms Catherine was just one of many survivors of the tragedy who were recounting their stories in public for the first time at a government-sponsored symposium in Jakarta two weeks ago on April 18.

She said that although her father was killed, she did not have to go into hiding unlike other victims of what has been described as one of the darkest periods in Indonesia's history. "I cried, saying I was sorry because I didn't know their pain was greater than mine," The Jakarta Post quoted her as saying in a report on April 19.

The Indonesian government has yet to apologise for the tragedy, toeing the line from the days of President Suharto, who had seized power after the failed coup and ruled Indonesia for 32 years.

However, President Joko Widodo, in an effort to begin a process of reconciliation and healing, had last Monday ordered his government to start documenting the locations of mass graves where victims of the massacre are buried.

Mr Phelim Kine from Human Rights Watch said Mr Joko's order is an act of political courage toward accountability that defies a half-century of official lies and denial.

"Establishing the location of those mass graves is a first step towards identifying the victims buried within and the circumstances of their deaths," he said.

The move, however, poses a threat to Indonesia's official narrative of the tragedy, which has long silenced survivors and family members of the victims, added Mr Kine.

While most civil and human rights activists welcome the Joko administration's endorsement of the public symposium, as well as the President's call to document the mass graves, many remain sceptical over how far the government will go in addressing the atrocity.

Their concerns seemed valid when Coordinating Minister for Political, Security and Legal Affairs Luhut Pandjaitan challenged claims at the April 18 symposium that more than half a million people died during the Red purge.

Mr Luhut, a retired general, also said that the government would not apologise for the 1965-66 saga due to the lack of evidence.

"During these decades we have always been told several hundred thousand people died, yet, until today, we have not found one mass grave," said Mr Luhut at a separate meeting with reporters that day.

The lack of historical records, however, has made it hard to establish the actual number of deaths during the crackdown.

While human rights groups often cite the 500,000 figure, which was first uttered by Mr Oeo Tjoe Tat, a Chinese-Indonesian official in the Sukarno government, estimates since then have ranged from less than 1,000 to as high as 3 million, reported The Jakarta Post last month.

These include figures derived from fact-finding groups as well as military reports.

Besides recognising the victims of the tragedy, Indonesian Science Institution founder Asvi Warman Adam said the current government must apologise. Referring to Mr Joko's popular moniker, the historian said: "Jokowi must resolve burdens of the past."