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Indonesia’s New President Has a Bloody History With Its Neighbor

Editor’s note: We decided to keep our special correspondent anonymous because of concerns about their safety.

At 82, Antonio Soares is blind and frail, carefully tended by his family. But time has not dimmed his memory of Sept. 7, 1983, the day that Indonesian soldiers arrived in Kraras, East Timor (also called Timor-Leste). Indonesia had occupied East Timor for nearly eight years by that point. Earlier that year, Indonesian forces had reached a tentative cease-fire with the remaining Timorese resistance.

But on Aug. 8, 14 Indonesian soldiers—who had allegedly committed murders and sexual assaults in the area—had been killed by Timorese guerillas, aided by local supporters. Now, weeks later, Indonesian soldiers were back for revenge.

First, they burned the village, sending the inhabitants fleeing to other villages and into the mountains. Over the next few days, Indonesian soldiers rounded them up. At the village of Buikarin, all men and boys older than 9, including Soares, were rounded up by Indonesian soldiers and marched off. The next day, at the Wetuku River in Tahubein, the soldiers lined them up and shot them.

Speaking to Foreign Policy, Soares says that he only survived because the people behind him were shot first, and the weight of their falling bodies flattened him to the ground. Indonesian soldiers called out, saying any survivors should stand up to be recruited as auxiliaries. Three men did, Soares remembers, and were unceremoniously shot. He survived by lying there for hours until he was sure he was alone and then fleeing into the forest.

Best estimates—based on reports from the independent Chega commission that conducted an investigation of crimes in the lead-up to and during the Indonesian occupation—put the number killed at the river at 141 people. Another 111 people were killed or disappeared in reprisals in the area in the following months.

Testimony and extensive research by expert scholars on Timor’s truth commission have linked parts of this massacre to an Indonesian special forces commander in the area. That man was Prabowo Subianto—who, on Oct. 20, aged 73, will be sworn in as Indonesia’s next president.

This might seem like a difficult pill to swallow for Timor. But while wounds linger, senior Timorese politicians have greeted Prabowo’s election cheerfully—some even suggesting that it might prove to be an unexpected boon for Timor. A policy of reconciliation—mortared by a mix of icy geopolitical realism, a fear of internal divisions, and perhaps a touch of idealism—explains why.

Prabowo was intimately connected to Indonesia’s occupation of East Timor, which lasted from 1975 to 1999. On Dec. 31, 1978, when he was still just a lieutenant, Prabowo led the squad that tracked down and killed Timor’s guerrilla president, Nicolau Lobato. Known as a brilliant soldier, Prabowo married the daughter of Indonesia’s President Suharto and rose quickly through the ranks of the Indonesian special forces but acquired a dark reputation.

His exact involvement in the events in Kraras remains unclear. One survivor interviewed by Foreign Policy, Alfonso Gomes, thought that Prabowo might have intervened to prevent the execution of a group of women and children that he was part of. However, several testimonies recorded by the truth commission suggest that Prabowo may have, at the very least, played a role in rounding up civilians in hiding, shortly after which several hundred were killed.

A number of analysts also believe that Prabowo played a key role in Indonesia’s notorious irregular warfare  strategy in the 1990s—sponsoring militias that terrorized the Timorese population. The final post-independence referendum rampage by these militias left some 900 people dead in 1999.

But Timor’s leaders have chosen to ignore that past. At the Shangri-La Dialogue in Singapore this year, Prabowo sat down for a friendly dinner with Timorese President José Ramos-Horta, who led the diplomatic effort for Timor’s independence. Prabowo himself acknowledged the incongruousness of it.

What Timor’s leaders really think remains unclear. A narrative of postwar reconciliation blankets all public statements about Indonesia made by Timorese politicians. Some observers feel this may be genuine, but others, speaking on background, recount seeing flashes of anger about Indonesia—and Prabowo in particular—among senior figures. And around election time, speeches in the local language, Tetum, can take fierier positions.

Still, there is no escaping the realities of Timor’s position.

“I think the Timorese leadership understood from day one that they needed to normalize relations, considering the size of Indonesia and its ability to be a source of instability which would have been way more costly for Timor-Leste’s rebuilding,” said Fidelis Magalhães, a former minister of the presidency of the Council of Ministers. This means, he says, laying aside any bitterness to behave rationally. “It is very difficult, but you have to do it for the greater good,” he added.

Squashed onto half of an island and with a population of 1.3 million and a GDP of $3.2 billion, Timor shares its only land border with Indonesia—population of 275.5 million and GDP of $1.3 trillion. In 2022, 27.1 percent of all Timor’s imports came from Indonesia.

Good relations with Indonesia mean benefits for Timor. Disputes over border demarcations have slowly been resolved amicably rather than degenerating into running arguments. Economic cooperation agreements have been signed. Scholarships to Indonesian universities are offered to Timorese students. And Indonesia is the staunchest proponent of Timor’s pending entry into the Association of Southeast Asian Nations.

Some even hope that Prabowo’s presidency might prove a strange boon for Timor.

“Maybe it’s better because he has some sort of relationship with Timor-Leste,” said Hugo Fernandes, the CEO of the Centro Nacional Chega, which preserves Timorese memories of the occupation. “Maybe the level of attention will be like when it was the time of SBY,” he added, referring to former Indonesian President Susilo Bambang Yudhoyono, a retired general who served in the Indonesian army in Timor.

Prabowo has a track record of turning former victims into allies. Some of the Indonesian student activists who soldiers under his command were accused of kidnapping and torturing in 1998 later became members of Prabowo’s political party, Gerindra.

One issue of particular interest for Timorese hoping for a better relationship is the location of bodies of Timorese killed by Indonesian forces during the occupation. To this day, many are still searching for the remains of family and friends, including the body of Lobato. With his personal connections and status within the Indonesian military, some think that Prabowo might be able to push for disclosure. Insiders hint that discussion of such issues is already quietly taking place.

But the price for steadily improving relations since 1999 has been giving up on accountability or compensation for many of the crimes committed during the occupation. “In the end, both sides decided to go more for friendship and a political solution and not to allow anyone to be tried by an international tribunal,” said Dewi Fortuna Anwar, a foreign-policy advisor to former Indonesian President B.J. Habibie, who allowed Timor the referendum on its independence, and later to SBY.

While the 2005 Chega! (“Enough!”) report—a meticulous 3,216-page report on human rights violations committed in Timor from 1974 to 1999—suggested that compensation be paid and all crimes be investigated, the Timorese government balked at pushing for this, according to insiders. To this day, Prabowo and the majority of other military leaders accused of involvement have never faced any legal investigation or process related to his actions in Timor.

What investigations did take place—by tribunals in Timor and Indonesia—only ever focused on crimes committed after the 1999 referendum on Timor’s independence, when pro-Indonesian militias launched their final rampage. Courts in Timor and Jakarta indicted a handful of individuals, but few have faced punishment, and those that did have were often then granted amnesties.

For some figures, such as Manuela Pereira, the director of Assosiasaun Chega! ba Ita, which advocates for female victims of the occupation, such an attitude is disappointing. “We were saddened and disappointed with our president who immediately invited Prabowo to visit Timor-Leste,” she said.

Pereira noted that while there is government support for veterans of the resistance and their relatives, support for victims—especially female victims of rape and sexual assault, of which there are many—is lacking. Many of her organization’s campaigns today focus on this.

However, while crimes against humanity are not subject to statutes of limitation, she said that the likelihood that many perpetrators will ever see a court has faded. Some victims used to campaign for this. “Now they are tired,” Pereira said.

Indeed, nine survivors of the operations around Kraras, when asked by Foreign Policy about what justice would mean for them, simply asked that the government offer support and opportunities to improve their lives.

When prompted, one expressed a desire to see Prabowo face trial, but he admitted that it would be very hard. When asked if they agreed with a policy of reconciliation with Indonesia, one interviewee praised it, while others showed signs of dissatisfaction. But all in the latter group still said that if this is what the government had decided, they must accept it.

A deep respect for leaders such as Timorese Prime Minister Xanana Gusmão, plus the dispiriting effects of time and poverty, might explain some of this. But digging too deeply into Indonesian crimes will also mean looking at the role of Timorese collaborators and the more questionable actions undertaken by the resistance, a sensitive topic in Timor.

In Dili, Celcio Soares, a university student, recounted how people seen as collaborators or coming from pro-Indonesian families still face discrimination. Despite coming from a family that opposed Indonesia’s occupation, he said that he cannot see this as anything but destructive. His own cousin is now in jail for murder, after an argument with someone from a family seen as pro-Indonesian turned violent.

The government has worked hard to try to keep such tensions under control, facilitating community reconciliation programs in the early 2000s and making space for figures seen as pro-Indonesian in the government. Not digging too deeply into the crimes of the occupation means not digging too deeply into the crimes of Timorese, collaborators and resistance fighters alike. To this day, Timor has not signed the United Nations convention on disappeared persons.

For some, this can be cruel.

“We will never reach the expectations of people who have been expecting for too long,” said Father Jovito Araujo, a Catholic priest and former commissioner on Timor’s truth and reconciliation committee, while speaking to Foreign Policy in July.

Many victims of the occupation remain psychologically tormented. Under such circumstances, said Father Jovito, forgiveness is hard, but more important than ever. “If you step over it, you will see new horizons. If you don’t, you will forever be in the shadow the past.”

And what about the accused perpetrators, such as Prabowo, who will never face accountability? “In the end we can only have faith in justice that is divine.”

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