Lindsay Murdoch – Antonio da Silva rarely smiles. His left ear has been cut off, his fingers broken and he has seen some of his militia friends killed during his fight to keep East Timor part of Indonesia.

But 41-year-old da Silva insists that his East Timor homeland will again become part of the Republic of Indonesia. "East Timor cannot stand alone," he says. "It cannot survive because it doesn't have the economic resources. Even with the help of the international community it has now there are serious problems."

As the United Nations makes the final preparations for East Timor to emerge as the world's newest nation when elections are held on August 30, da Silva says he is making sure that a new generation of Timorese children see things the way he sees them – from Indonesia's perspective.

Defying UN conventions protecting children, da Silva last month helped separate 46 children aged between six and 12 from their parents in refugee camps in West Timor and escorted them by ship and bus to a privately owned dormitory in the hills above the Indonesian city of Yogyakarta in central Java.

Humanitarian workers suspect that pro-Jakarta Timorese living in Java want to indoctrinate the children as activists to push for East Timor's eventual reintegration with Indonesia. The Hati Foundation, an organisation led by a prominent Timorese activist, Octavio Soares, has now transported almost 200 Timorese children from the camps since 1999 and placed them in orphanages or institutions across Java.

Death threats that Soares made early this year to UN officials forced them to abandon efforts to reunite some of the children with their parents, who have returned to East Timor from the West Timor camps controlled by pro-Jakarta militiamen, including da Silva.

Surrounded by the newly arrived children at the Yogyakarta dormitory, Soares says he "doesn't give a damn" about the UN or the Indonesian Government, which never gave him permission to take them from West Timor. "My responsibility is to the [Timorese] community," he says. "The more money I have, the more children I will bring out. I will bring 10, hundreds or thousands if I can."

Almost two years after militiamen, backed by Indonesian police and troops, rampaged through East Timor in an orgy of violence and then forced 250,000 Timorese across the border, alarm bells are ringing about the possibility of a sustained campaign to destabilise East Timor.

Indonesian officials this week released the results of a two-day canvass showing that 98.02 per cent of 113,794 Timorese refugees stranded in West Timor had opted not to return home. Foreign observers greeted the results with scepticism, pointing out that the camps are still under militia control, leaving anyone who opted to return open to reprisals.

"People who may not have given up hope of seeing East Timor join Indonesia have access to 100,000 people to use for whatever purpose," says a UN official who asked not to be named. "These people are not returning as we thought most of them wanted."

Unless the camps are cleared UN peacekeeping troops – many of them Australians – will have to stay dug in along the East Timor side of the border, diplomats and analysts say. Soares, an Indonesian-educated medical doctor who speaks four languages, skirts the question when asked whether his motive for taking the children out of the camps is part of a plan to capture East Timor back for Indonesia.

"That's a very sophisticated story about me," he says. "Oh, so I can indoctrinate some person? For 23 years, Indonesia never succeeded in indoctrinating all the East Timorese. How come a stupid, ordinary person like me can indoctrinate people?"

Soares says that "maybe some journalists think that because I'm Indonesian, I would indoctrinate the kids ... But you know what? It's not that easy to indoctrinate them. Even Jesus Christ can't make every man believe in him, right?"

Soares says that if East Timor again became part of Indonesia, he would not go back. He says his Portuguese ancestors did the wrong thing by East Timor and he would like to help the Timorese, especially the children, as an apology.

Calling the children he has brought out from the camps "my children," Soares becomes agitated when told that parents interviewed by The Age who have returned to East Timor want their children returned. "Yes, I read that," he says. "But it's a stupid thing. I wasn't that stupid when I first came to them [the parents] and informed them about the kids going to study in Java."

Soares dismisses the stand of the United Nations High Commissioner for Refugees that children should never be separated from their parents in times of conflict or upheaval, except in extreme circumstances.

Referring to 120 children he left at Catholic orphanages near the Indonesian city of Semarang in late 1999, Soares says: "The children can decide for themselves how they would like to live. They can hear. They can understand. The children have already been knitted to the environment. They can feel it. They will say, 'I want to stay here [at the orphanages] in good condition. I'm healthy. I'm safe. Why should I go back? Okay mother, if you love me, why don't you just come and see me here?'"

Soares admits that he has lost his temper during talks with UN officials. "I am a bad guy," he says. But he then asks: "What do they say about me? Do they think I am a lunatic?"

Bearded, wiry and hyperactive, Soares produces pro forma documents he says have been signed by the parents of the 46 children at the Yogyakarta dormitory that has just been opened by a 70-year-old retired Indonesian Education Department lecturer. Soares denies claims that forms supposedly signed by parents of the other children were fraudulent. "Yes, all the parents gave their approval. They need to declare their approval openly in front of the community."

UN officials who have been trying to reunite some of the other children with their parents were not aware that a new group had left the camps until contacted this week by The Age. The UN has banned its officials working in West Timor since three UN aid workers were murdered by militiamen in the border town of Atambua in September last year. This has prevented them asking the parents of most of the children who have been brought to Java whether they would like to be reunited with their children.

Officials and humanitarian workers are worried that the longer the children stay under Soares' influence, the more traumatic it will be to reunite them with their families. Some have already forgotten their parents' names. Catholic nuns caring for the 120 children at five orphanages near Semarang say many of them are deeply traumatised and confused and sceptical about UN assurances that their parents want them to return.

Friends of Soares have confiscated letters sent by many of the parents, humanitarian workers say. The nuns too, have been unsure of UN assurances that it is safe for the children to return to East Timor and that the parents want them back, placing them at the centre of a tug-of-war between Soares and the UN.

In an attempt to convince the nuns, the UN recently flew three of them to East Timor meet the parents. But Soares seems to think he knows best about the children's future. "The nuns came to me when they returned," he says. "They said to me, 'sorry, we signed something in East Timor.' But I know that the UN blurred the situation. It is not as they saw it. Not as it was explained to them."

Soares then launches into a tirade against some of the parents, accusing one father of rape and others of being "too stupid" to take care of their children. "If I gave the parents money, they would spend it all in one day," he says. "My aim is clear ... I'd like to do a little bit for the East Timorese because they are stupid, poor and neglected. So when I die, my great, great grand-children will remember me as a good person ..."

Soares, whose uncle, Abilio Soares, was the former Jakarta-appointed governor of East Timor, left the territory at the height of the militia violence in September 1999 and has not returned. He says he has read reports that international non-government-organisations want to quit East Timor because of the situation there. "There's no hope for East Timor to live," he says.

"Because the big countries that said they would help, like Australia, did nothing. People sit in Darwin, Sydney and Melbourne and look at East Timor and say, 'die you East Timor, die you'."

Whenever Soares speaks, the children have been told to stop whatever they are doing and listen carefully.