Indonesian soldiers used rape as a secret weapon, but their "orphans: bear silent witness. Louise Williams and Leonie Lamont report.

Sister Maria leaned forward and quietly confided the truth about the Catholic orphanage which lies along the lonely northern coastal road of East Timor: "Most of the children are mixed race, the babies of women raped by Indonesian soldiers."

This is not a truth openly voiced in East Timorese society. Instead, said Sister Maria in an interview in Dili earlier this year, the children were raised by the Church. But, while they are not openly rejected, everyone knows the shame of their parentage.

In the early years following the Indonesian invasion, orphanages were filled with genuine orphans: so many adults had been killed in military operations. Now, Sister Maria said, most are children of rape, a tactic used over and over again in war, usually to hurt the father or husband of the victim. The woman's own suffering is an afterthought in a war between men.

"One young woman I knew had four babies, I kept asking her why this had happened again and she just said there was nothing she could do," she said. Sister Maria's own whereabouts remain unknown, following the rampage through Dili and the murder of Catholic nuns and priests.

Rape, according to a report released this year by Ms Radhika Coomaraswamy, the United Nations Special Rapporteur on violence against women, has been systematically used by elements of the Indonesian military in East Timor, Aceh and Irian Jaya.

"Rape was used by the military as a method of torture and intimidation against the local population. Relatives of political opponents were raped by the military as a form of revenge, or to force the relatives out of hiding," she said.

"Much of the violence against women in East Timor was perpetrated in the context of these areas being treated as military zones ... rape by soldiers in these areas is tried in military tribunals, and not before an ordinary court of law."

Under Indonesian law, for a rape to be prosecuted it required corroboration – including the testimony of two witnesses. Women lived in a "realm of private terror", for any victims or witnesses who dared to take action were intimidated with death threats, Ms Coomaraswamy reported.

"Many of the women who were raped as virgins are single mothers who have suffered stigma in their communities after giving birth to children of Indonesian soldiers ...

"Some of these children are the result of rapes, others are the product of a situation that resembles sexual slavery and some are the result of consensual sex ... the women are having a very difficult time, not only because of poverty, but because the sight of these children often reminds them of rape." She said the Indonesian state should take responsibility for these children.

Senator Marise Payne, one of the parliamentary members of the Australian observer delegation to East Timor, said she had been told of soldiers picking attractive girls from the villages, and making them their "playthings". "This has been happening for 20 years," she said.

A Catholic nun, Sister Tess Ward, said: "Many women have said to me they feel dirty, and are too ashamed to tell people."

"I don't know of anytime when women were game enough to tell the police. Many of the people said to me the only people we can talk to is the priest or sisters.