In 1998 Suharto was forced to resign and the New Order’s tight grip on East Timor suddenly loosened. In January 1999, the new president B.J. Habibie offered a referendum where the Timorese could vote to accept autonomy under Indonesia, but it was roundly rejected by the East Timorese. Even though the New Order regime had come to an end, the Indonesian military still had a lot of influence in East Timor and was displeased with the result of the vote. In the lead-up to the vote it trained East Timorese as militias, and after Indonesia’s loss it gave them a free reign. The military and the Timorese militia killed many supporters of independence and looted and destroyed the territory. One-third of the population was forced to leave East Timor. The reason for displacement seems to have been to demonstrate that a sizable percentage of the population rejected the results of the referendum and feared living under a government controlled by those who had opposed Indonesian rule. Many of the displaced East Timorese quickly returned home, but tens of thousands of East Timorese still remain in Indonesia. Many were civil servants or had worked for the security forces and still have secure jobs. Others have committed violence and are afraid to return home.
Some were ideologically opposed to independence. A few of these decided to take children to institutions in Indonesia and educate them as East Timorese who believed that East Timor belonged within a united Indonesia. In the immediate years after the referendum they seemed to believe that they could raise a generation who would share their hopes and take up their struggle to re-unify East Timor with Indonesia.
They came to the camps in West Timor, and to a lesser extent in South Sulawesi, with promises to parents to take and educate their children and return them later, just as soldiers and others had done throughout the occupation. The conditions in the camps in West Timor were particularly appalling and many parents agreed to give their children to those who made these promises. The UNHCR estimated that there were approximately 1000 children separated from their families after the referendum. 
What is interesting is that the main actors in these transfers often had themselves been sent to Indonesia when they were children. Here we offer a brief sketch of some of them. The Indonesian and international media paid considerable attention to these separated children and we provide links to a few of these articles which appeared in the media.
- Hasan Basri and Lemorai Foundation
- Mohammad Johari and the Al-Anshar child care institution
- Hati Foundation and the Soares family
- Cinta Damai Foundation
Hasan Basri and Lemorai Foundation
Hasan Basri was born Roberto Freitas in Lalea, Bacau district of East Timor. When he was still a young child he was influenced to convert to Islam by the Indonesian soldier he worked for and he took his Islamic name. In 1980 Salim Sagran, the founder of Yakin Institution, took him to the Darul Istiqomah Pesantren in Maccopa sub-district, about 25 km from Makassar in South Sulawesi, to receive an Islamic education. Later Basri returned to East Timor where he helped send other children to Islamic institutions in Indonesia and also worked for Indonesian intelligence.
In 1998 he established the Lemorai Foundation in Bandung, West Java. With the announcement of the referendum in East Timor he offered relatives and acquaintances from his village to take their children to safety in Indonesia and give them a free education there. He cared for them through his foundation and also found other local institutions that would take in children. In 2002 he told a foreign journalist that he had assisted 661 East Timorese to move to Bandung, many of them children. He claimed he placed almost one hundred children in small groups in a dozen institutions in Java, South Sumatra and Sumbawa. He set up his own pesantren in Gunungmanik, Tanjungsari, Sumedang, West Jawa, where he took many of the East Timorese children.
However, when East Timorese parents returned to East Timor, Hasan Basri refused to return the children in his care. He insisted the parents had to collect them and would not allow the the United Nations High Commission for Refugees, UNHCR, to facilitate the children’s return home. The father of Nur and Johnny, in the care of Hasan Basri, travelled from East Timor to Bandung to find his children in mid-2002. However, Basri refused to meet him, and the father returned to East Timor without even seeing his children. For a long time Basri did not even tell the children about their father’s visit.
He did all he could to keep the children in Indonesia—those he had brought himself and others sent by Yakin in earlier years and still living in the Bandung area. For some years after the separation of East Timor from Indonesia he received financial support from some Indonesians who were angry about the loss of their former territory.  Efforts by the media, including international media, demanding that he return the children gave him a forum to declare his allegiance to Indonesia. He needed to keep children in his care as the new converts helped him solicit funds for his foundation. But the real burden was borne by the children and their parents who were forced to accept his assertions that they had been handed into his care so the children had to stay with him until their education was complete.
In the media:
- Watch Youtube video: ‘East Timor`s stolen children’, David O’Shea, Dateline, SBS Australian, 4 September 2002
- Timor’s lost boys,Simon Elegant, Time, 23 December 2002
- Mereka memilih tetap tinggal di Sumedang: 53 warga eks Timtim menolak dipulangkan, Pikiran Rakyat, 11 October 2002
- Kampung Muslim Timor Timur di Sumedang, Kompas, 12 Desember 2002
Mohammad Johari and the Al-Anshar child care institution (Panti asuhan Al-Anshar)
Mohammad Johari was born in 1962 with the name Bonifacio Moreira. He comes from Uaitame, Quelicai, Baucau district of East Timor. After the invasion his father worked as an assistant (TBO) for the Indonesian military. After Bonifacio completed elementary schoool he moved to Dili and he decided to learn Indonesian so that he could become a civil servant. He also decided to convert to Islam and took his new name. In 1984 Yakin sent him to study in Makassar.
After completing his education he returned to East Timor and worked alongside Indonesian preachers in the districts of East Timor. He also helped Yakin gather children to send to institutions in Indonesia.
In the early 1990s he decided to set up a place in Makassar for East Timorese to live together while they were attended school. He thought this would better meet the needs of East Timorese and also help them overcome homesickness. His Al-Anshar institution received financial support from mosques and local businesses and a generous donation from the Japanese government. Mohammad Johari also traveled regularly to East Timor to collect children for his own institution, offering them a free education in Indonesia.
In 1999 Abdurrahman Alberto had taken over the administration of Al-Anshar institution from Johari. He was also one of the East Timorese sent by Yakin to the Maccopa institution in Sulawesi in the early 1980s, along with Hasan Basri. After the referendum in 1999 Abdurrahman and several other associates traveled to the camps in West Timor to collect children for their institution in Sulawesi. The institution also took in the children of Muslim families who fled East Timor after the vote. Johari also asked other nearby Islamic institutions in South Sulawesi to take in East Timorese children. By 2008 few East Timorese Muslims had returned to East Timor and many settled on government transmigration sites in South Sulawesi (Jakarta Post 2002a).
When the parents of children in Al-Anshar institution returned to East Timor, the organizers of Al-Anshar refused to allow the UNHCR to take the children home. Just like Hasan Basri in Bandung, they used media demands to return children as a platform to make nationalistic pronouncements of their support for Indonesia and rejection of independence for East Timor. The rights of the children and their parents were not their main priority.
When the UNHCR came with several parents and took four children home, the institution led protests by ‘pro-integrationists’ in Sulawesi who accused the UNHCR of kidnapping the children. The institution demanded ‘compensation’ for the years it had cared for the children, further evidence that one of its prime motives in holding the children was financial.
In the media:
Jepang bantu Yayasan Al-Anshar Timor Timur di Ujungpandang, Suara Pembaruan, 18 July 1997 (Translation: Japan helps ‘Al-Anshar Timor Timur’ Foundation in Ujungpandang) Indonesian language:
- Pengungsi Eks Timor-Timur Tuntut Ganti Rugi Rp 50 juta, Tempo Interacktif, 11 Juli 2003
Hati Foundation and the Soares family
The family of the last governor of East Timor, Abilio Osorio Soares, were ardent supporters of integration. After the referendum they established the Hati (Hope for Timor) Foundation, (Yayasan Harapan Timor – Yayasan Hati). They planned to send many thousands of children from the camps in West Timor to Central Java to be educated in institutions run by the Catholic Church. The foundation claimed that it wanted to help the families because of the desperate situation in which they lived in the camps. Their motives were highly ideological and not financial in comparison with those who ran the Islamic institutions. They planned to educate the children as East Timorese who supported re-integration with Indonesia.
The governor’s nephew, Octavio Soares, organised the transfer of the children to Java. Hati Foundation members knew that the ADKS nuns in St Thomas institution near Semarang had taken in East Timorese children in 1977 (the 20 children including Petrus Kanisius) and in 1999 they asked the nuns again for help. In late 1999, 123 young children arrived in Central Java and the following year a further 46 children. However, in 1999 the Indonesian Catholic Church had changed its position in relation to East Timor and no longer gave nationalistic support to integration. It refused to accept any more children from Hati Foundation in its institutions and divided the children already in its care among various institutions in Java to make it more difficult for Hati Foundation members to supervise and indoctrinate them.
However, for several years Hati Foundation received tacit Indonesian government and military support to carry out its agenda. The organisers repeatedly frustrated attempts by the UNHCR to return the children. They intimidated the children making them fearful of what might happen if they went back to East Timor. As a consequence, some children even refused to go home with their parents who came to collect them.
This group of separated children received a lot of attention in the Indonesian and international media. Many children returned to their parents in East Timor. The parents of others now live in West Timor. Some of these children find it is difficult to understand why they can’t return to their land and homes in East Timor—they have been fed so much misinformation. In 2009 a small number had completed high school but could not continue their education in Indonesia as their nationality status was unclear.
Reports by Australian journalist Lindsay Murdoch in the Sydney Morning Herald (SMH) and The Age (Melbourne) drew a lot of attention to the situation of the children.
In the media:
- The stolen children of Timor, SMH, 25 October 2000
- Fear bars family reunion, The Age, 17 March 2001
- Timor parents beg for their stolen children, The Age, 24 April 2001
- The stolen children of Timor, SMH, 27 April 2001
- The man who brainwashes children, SMH, 18 June 2001
- Activist snatches 12 children on way to family reunion, SMH, 7 August 2001
- Timor leaders seek world help for seized children, The Age, 27 August 2001
- Pressure on Jakarta over children, SMH, 28 August 2001
- Jakarta urged to reunite children with parents, The Age, 29 August 2001
- Tense reunion for East Timorese families, The Age, 17 September 2001
- Repatriation of children to E. Timor meets resistance, The Jakarta Post, 4 July 2002
- 1500 Timorese children still stranded, The Jakarta Post, 6 July 2002
- 134 Pengungsi Anak Timtim di Jateng, Suara Pembaruan, 25 Februari 2001
- 46 Anak Timtim diasuh di Gunungkidul, Kompas, 10 Juni 2001
- “Rai Timor,” Anakmu di Gunung Kidul, Kompas, 20 Juni 2001
- 10 Anak Timtim bertemu orangtuanya, Jogjakarta edition, 15 September 2001
- Reunifikasi Anak Timor Timur (1): Terganjal kecurigaan Yayasan pada UNHCR, Suara Pembaruan, 14 October 2002
- Reunifikasi Anak Timor Timur (2): Jangan Sekadar Manuver Politik, Elly Burhaini Faizal, Suara Pembaruan, 15 Oktober 2002
- Reunifikasi Anak Timor Timur (3-Habis): Demi Kemanusiaan atau Agen Asing?, Elly Burhaini Faizal, Suara Pembaruan, 16 Oktober 2002
Cinta Damai Foundation
An East Timorese Protestant minister, Rev Paulus da Costa, from Matata in Ermera district and Cornelius Banoe a business man from Kupang who lived in Matata until the referendum set up the Cinta Damai (‘Love Peace’) Foundation to send children for an education in West Timor. It was not an official program of the Protestant Church in Kupang or of the Protestant Church in East Timor, the GKTT, Gereja Kristen di Timor Timur.
During the 1990s it sent approximately sixty children to West Timor. The children were cared for in the child care institution associated with the Gereja Masehi Injili di Timor (GMIT) Oeba Ebenhaezer Protestant Church in Kupang. Cornelius Banoe also placed some of these children in foster homes in West Timor, where they often worked as household servants in exchange for their school fees. Some children worked as street sellers and as farm labourers, and not all attended school.
After the referendum, Rev Paulus da Costa, and Cornelius Banoe visited families from Ermera living in the camps in West Timor and promised to educate their children. Some parents agreed and Cinta Damai Foundation took 59 children into its care. However, the organisers did not place the children in the institution run by the Protestant Church as the parents had thought they would. Without seeking the consent of parents, Cornelius Banoe made a radio announcement asking individuals to offer to care for a child. Most of the children were taken in by families in Kupang. Parents were angry when they discovered that their children were not living at the GMIT institution, as had been agreed. When they returned to East Timor they demanded that their children be returned.
By 2004, most but not all of the East Timorese children given to families in Kupang by the Cinta Damai Foundation in 1999 had been located; and half of the children sent from East Timor by the foundation before the referendum had returned home, while the others were still in Kupang. However, some, like, Ago Pito (Jon dos Santos), fell through the net. He was about seven years old in 1999 when his parents handed him into the care of the foundation, but in 2007 he had lost contact with his family and was a street seller in Kupang. He believed that if his parents were still alive they would have come to find him.
The motivation of Cinta Damai Foundation was similar to that of Islamic organisations which sent children to Indonesia. It wanted to help the children from impoverished families but also to show their support for integration. Also like the organisers of the programs to send children to Islamic institutions, they betrayed the trust of parents and were dismissive of parental rights.
The UNHCR was able to repatriate many of the children taken in 1999, however, it was often a complicated process. Besides the children we have already referred to, there were also children separated from their parents through informal adoption processes and family breakdown. In earlier yeas a child might have been given to family member, perhaps a sister who had no children of her own. After 1999 the biological parents or the adoptive parent moved to Indonesia. The links that biological parents expected to maintain with their children were broken. The stress and ideological divides often led to family breakdown, with the result that in some case one parent remained in East Timor, while the other moved to Indonesia. Custody of the children was contested. The division between East Timor and Indonesia made it more difficult and also expensive for parents to visit and collect their children in Indonesia. Other children were held by former militia members who refused to hand over the children. 
Once a child reaches 18 years of age the UNHCR no longer searched for them. Many remain forgotten in Indonesia, such as Ago Pito in Kupang who believes that if his parents were still alive they would have come and collected him. 
1. Evaluation of UNHCR’s repatriation and reintegration programme in East Timor, 1999-2003, United Nations High Commissioner for Refugees: Evaluation and policy analysis unit, 24 February 2004, page 60.
2. Mereka memilih tetap tinggal di Sumedang: 53 warga eks Timtim menolak dipulangkan, Pikiran Rakyat, 11 October 2002
3. Family will not give up hunt for daughter’, Lindsay Murdoch, The Age, Melbourne, 12 February 2006.
4. ‘Eight years after 1999: Displaced East Timorese children go hungry in Indonesian West Timor’, Elcid Li, Inside Indonesia 90: Oct-Dec 2007.