Tom Hyland – The struggle for East Timor was played out in the battle for its children, a landmark report has found.

Some were abducted by departing soldiers, smuggled out in crates. Others were taken from orphanages. Some parents were forced or tricked into handing their children over. Other parents voluntarily sent them away, hoping they would be cared for, educated and returned home.

Some never came back and grew up not knowing their families, their language, religion or culture. They are East Timor's lost, stolen generation.

Aidia is the mother of one of them. Thirty years on, she clings to hope. She's middle-aged now, old by East Timor standards. Her child, if she is still alive, would be in her 30s, maybe with children of her own. Aidia last saw her daughter Kustantina in an Indonesian army office some time after 1975. The child was three at the time.

With his tour of duty at an end, an Indonesian soldier told Aidia, a widow living in a forced-resettlement camp, that he had no children of his own. "I would like to take her home (to Indonesia)," the soldier said. "I want to give her an education and after that she can come back." She never did.

Aidia is illiterate. It was at the height of Indonesia's invasion, savage war was raging and she feared soldiers. In the army office, she pressed a thumbprint onto documents she didn't understand. When the paperwork was done, the soldier, his bags already packed, left with Kustantina, and a family was torn apart.

"I only gave away my child because I was afraid. They had guns and I felt like I didn't have a choice," Aidia says. She doesn't say what she has endured in the years since. It is a gap that speaks of an aching, anxious longing.

"I live now with the hope of that man's promise that one day my child will come back to me ... I often go to the edge of the sea, breathe in the fresh air and remember my child taken from me across those waters."

Aidia's story is told in a landmark report on East Timor's ordeal under Indonesian occupation. The 2500-page report by the Commission for Reception, Truth and Reconciliation – entitled Chega! (Enough! in Portuguese) – documents in harrowing detail a quarter-century of war, massacre, torture, forced relocations, starvation and systematic rape.

Children were not spared. They were forced to serve on the battlefield and died in massacres, as well as from bombardment and famine. They were tortured in detention. Girls as young as 14 were raped and forced into sexual slavery as "comfort wives" during a time when soldiers could rape at will. And then there were those who were simply taken away.

The commission finds both sides in the conflict failed to protect children "but the most reprehensible violations of all kinds were committed by Indonesia".

A unique dimension to the children's suffering is now revealed for the first time. An unknown number – the commission estimates thousands – were taken to Indonesia. They may have escaped the ordeal of those left behind but they and their parents paid a different price.

Some were taken from combat areas after their parents were killed or they became separated from their families, the report says. The commission heard evidence of hospital staff hiding children to prevent their removal.

It heard of an eight-month-old girl called Veronica, taken by a soldier who said he had no daughters of his own. In payment he gave the mother a bag of rice.

Some mothers resisted. One girl identified only as QN was abducted from Ermera by an army officer and taken to Dili in a box. Her frantic mother traced her to an army office in Dili, where, despite being kicked by soldiers she rescued the child.

But the story has no happy ending. Back in Ermera, the officer raped two of QN's older sisters, one of whom subsequently gave birth to a girl. He subsequently "took this baby girl with him back to Indonesia. No news of the child's fate has ever been received by the family."

Nobody knows how many were taken, but the commission is confident "several thousand" children were involved. The removals "took place along a spectrum from unregulated transfers ... without consent being sought, to coercion ... to informed consent". An unknown number of the children – many of them adults by now – have yet to be identified.

The commission finds "insufficient evidence" to say if the removals were official policy. There is evidence some officers tried to stop lower-ranking soldiers smuggling out children. But at the same time, it says officials at the highest levels, extending to former president Soeharto and his family, were involved in unregulated removals.

The worst stories come from the harshest early years of the occupation, between 1976 and 1979, when a "climate of chaos, coercion and impunity" created conditions for widespread removals.

Maria Legge Mesquita was taken by soldiers after her father was killed. She told the commission: "When the army was ready to leave, after their tour was over, they took five children, including me, and put us in crates. We were put in crates, one per crate, like chickens." She was lucky. A local family, fearing its children were being taken, freed Mesquita and the other children.

Soldiers also took children from orphanages at a time when East Timor had an estimated 40,000 orphans. They preferred light-skinned children, according to former governor Mario Viegas Carrascalao. "They liked children with mixed blood. They were the ones that they took to Indonesia."

Many of those taken were young boys pressed into army service as "TBOs" – the Indonesian acronym for "operations assistants" who carried ammunition and supplies.

One TBO, Alfredo Alves, told how, at the end of his unit's tour, he was placed in a box so officers wouldn't see him being loaded on the departing ship.

"After half an hour we were allowed to get out of our boxes and I saw Dili fade into the distance. I felt very sad because I had not seen my mother since I was taken from the schoolyard in Maubisse. This happened in February 1980, when I was 13 years old."

By the 1980s, officials sought to regulate removals to ensure there was parental approval, but the report concludes that, "in the prevailing climate of coercion", there was no guarantee parental permission would be freely given as "there was almost always an element of duress".

It was not only soldiers; government officials and charities took part. While these removals were better organised, with the stated intention of caring for children, many were taken without parental permission. Nor could parents maintain contact with children once they were taken.

Soeharto family foundations played a prominent role. In one notorious incident in 1977, 20 children were taken without their parents' knowledge to Indonesia. Before being sent to an orphanage, they attended a presidential welcome where Soeharto declared: "You are our children, owned by the state, and we will be responsible for your welfare from now on."

By the 1990s, when Jakarta faced a growing revolt by East Timorese youth, the government started programs to transfer children to Indonesia. While officially aimed at increasing education and job opportunities, the program had "underlying political and social motivations" of encouraging a commitment to integration with Indonesia and removing potential trouble-makers from East Timor. It was part of the battle for the hearts and minds of the young.

The entire struggle for East Timor "was partly played out in the battle for its children", the report says. "The widespread practice of removing children displayed a mindset that, by taking control of (East Timor's) territory, Indonesia also gained unfettered control over its children."

Even where transfers had a humanitarian motive with parental consent, little effort was made to ensure children could maintain contact with their families or return home. Some never saw their families again. Some of the children prospered in Indonesia, adopted by families that loved, cared for and educated them.

But such cases shine feebly in the unremitting gloom of the commission's report. A common thread runs through the children's experience: the loss of cultural identity, their language, their names. Some, taken as babies, were never told they were East Timorese.

For some this loss and alienation is a wound that never heals, even when they try to re-connect with their homeland.

One boy, taken from a Dili orphanage when he was five years old, was one of 10 children sent to a state orphanage in Bandung, Java, in 1979.

"I was living in a foreign environment," he says. "We never spoke about Timor, we couldn't speak (the Timorese language) Tetum, and we didn't send letters to Timor. We were brought up as (Indonesian) children in Java. I didn't know why I was there, just that there had been a war in Timor.

"I was happy to get an education in Bandung but I felt in my heart that I would always be someone wondering who he really was. I actually felt like I had been brainwashed. Eventually I made friends from Timor but I felt backwards and embarrassed around them because I couldn't speak Tetum. I often had to leave the room or more often I was silent. I tried to study my own language and culture.

"Living without my family was also very bitter for me. Very bitter. Even now if I see a picture of a mother holding her child, tears well up in my eyes. It is so sad that I cannot ever feel close to my family."

[The full CAVR report is at http://www.ictj.org.]