Some were taken by soldiers and others were sent by government and religious organisations.
It's not a simple story.
In many cases, the children were taken against their parents wishes and were treated like slaves in their new homes.
But others were saved from almost certain death in conflict zones and went on to receive an education unattainable in East Timor.
Helene Van Klinken has recorded the first account of this period in her new book called 'Making them Indonesians - Child Transfers out of East Timor'.
Correspondent: Joanna McCarthy
Speaker: Helene Van Klinken, author
VAN KLINKEN: I first heard about this when I was living in Indonesia, but basically the idea of taking it up as something that needed to be researched was while I was working for the Truth Commission in East Timor, the CAVR, in 2003.
McCARTHY: And you make the point in your book that there were a range of motivations behind these removals. Can you tell us about that?
VAN KLINKEN: The motivations were varied. Of course everybody said that they wanted to help the children and but there were other reasons why people took children. Some of them wanted to because they didn't have children of their own, individual soldiers and civil servants, some of them wanted to have a child of a particular sex, they had all boys and they wanted a daughter, some of them took children because they could work for them and that's not an uncommon practice in Indonesia, but children those cases are often exchanged between family members, but in this case it was often people they didn't know or particularly soldiers. Not all the children were sent into private homes adopted by individuals. Many were sent to institutions and a lot of children were sent to Islamic institutions throughout Indonesia, small groups right throughout the archipelago and they were being offered an Islamic education. So probably to help increase the number of Muslims who were living in Indonesia just like many other religious organisations did. So despite these motives, there were always an underlying motive that they wanted the children to become like a called the title of my book to "Make them Indonesians" and to get East Timor to accept their status as part of or its status as part of Indonesia. And very often in such colonial projects, people start with children, because they are more easily impressed. Of course there were many children or older children who were sent for an education, but the children that I write about were younger children, dependent children, who couldn't make contact with their families themselves. They were dependent on the people who cared for them in the institutions or in the homes where they lived.
McCARTHY: And was this officially-sanctioned Indonesian policy or was it something that occurred more on an ad hoc basis?
VAN KLINKEN: In some ways it's both, because on the cover of my book. I just showed you the picture of the president of Indonesia at that time President Suharto and his wife who are entertaining at their private home a group of 20 East Timorese children. He had an organisation that was set up by him specifically to help East Timorese and it started off in that way. And that organistion organised the transfer to Indonesia of about 61 young children. They were sent to Bandung and to Central Java. So one of the group of children that he brought to Indonesia. He took them to his home and invited the media there to see the children and they talked about the children in the media. It was right at the time that the president was offering an amnesty to the resistance, the Fretilin resistance, and I think it was a way to show that Indonesia cared for East Timor and if you join Indonesia, we'll care for you, like we are caring for these children and in a way the Indonesians treated in many ways treated these East Timorese as children. So this picture really summarises or sort of conveys the meaning of what I'm talking about in my book.
McCARTHY: And you did have the chance to meet with and speak to adults who had been sent to Indonesia as children. How did they describe their experiences?
VAN KLINKEN: Very mixed, some had good experiences in their homes, particularly those who were taken by soldiers or individuals who didn't have children of their own and then they treated as their own children equally with children or as they would their own children. For others, they had to work hard in their adoptive home and you may know or your listeners will know about Alfredo Alves Reinado. He was one of these children and I talk about him in my book, about his experience of being sent to Indonesia and he was badly treated in Sulawesi and he ran away, so there's a very big difference in the way many of the children were treated. So it depended on the individual who took them.
The children in the institutions knew that they came from East Timor because part of the aim of the exercise was to send them back to East Timor and to help with development in East Timor, or to help convert others to Islam. But for the adopted children, it was a bit different. They were taken there and they were raised as Indonesians.
McCARTHY: And for the parents whose children were transferred, whether they gave their consent or whether it was forced upon them. They must have grieved for the rest of their lives. Did you have the chance to speak to any parents?
VAN KLINKEN: Yes, absolutely and one woman had an adoptive document, a letter of surrender that she carried with her all her life. She carried that through up to and even in '99 with her when she had to flee into the mountains. Also, through all the difficulties that she faced, she carried that adoptive document, that letter, because it was so important to her and that's the case with others. Some tell me how they sat, made a table, a place at the table for the missing child believing that one day the child would come home and fill that place.
McCARTHY: It's heartbreaking.
VAN KLINKEN: Yes, yes, yes.
McCARTHY: And have their been family reunions since?
VAN KLINKEN: There've beeen some, yes. A few that I know of but there have been a few cases where children Biliki who I begin my book with the story of Biliki and she was taken as a six year-old, seven year-old child to Indonesia by an Indonesian soldier, from her family in Ainaro and she threw a handkerchief out the window of the helicopter at the door of the helicopter as she took off. That's probably the only thing that she had and she just remembers the screaming of being taken away. She was taken to Jakarta. She was educated and she's grateful for the education she got. I met her in 2003 and she'd just wanted, she was still desperate to find her family and I was able to... the CAVR, The Truth Commission broadcast her story on their radio program and she was able to reconnect with her family.