Chris McCall, Jayapura – It is a crude report from one tiny area of the Indonesian province of Irian Jaya.

It lists 614 people who all died violent deaths between 1969 and 1998. In the column for "doer", all entries contain the word "Abri", an abbreviation for the Indonesian military.

It is a local initiative in the central Paniai region of the province, put together by locals with help from church groups. It is not comprehensive, not independent and needs verification.

But each entry includes a name, an age, a year of death, plus details of gender, tribe, marital status and village. There are one or two gaps, but too few to be significant. This is clearly a report based on evidence from witnesses.

It poses a question. If so many died in such a small area, what has happened all over Irian Jaya – called West Papua by those supporting separatism – since the United Nations gave it to Indonesia in 1963? Human rights groups are uncovering fragmented evidence of a hidden holocaust, concealed by remoteness, restrictions and lack of interest by the outside world.

Aloy Renwarin, vice-director of the Papuan human rights lobby Els-Ham, says there are strong suggestions that the number of victims of Indonesian rule in Irian Jaya may equal or exceed that in East Timor.

Human rights groups in East Timor contend that around 200,000 people died from war, famine and disease between 1975 and 1999, the years Indonesia invaded and finally left. Although just a best guess, there is consensus now that the figure roughly reflects the underlying truth.

Mr Renwarin is careful with his information. He admits he does not have the hard data to back up the claim, but the indications are there in things like the Paniai report. "What is clear is that the number may be more than in East Timor. It is clearly about the same or even more. But no one works seriously on it," he said. "Everyone is still scared. An example is Theys' death."

Separatist leader Theys Eluay's flamboyant leadership put his face on newspapers and television screens outside Indonesia, gaining a profile for Irian Jaya it had rarely enjoyed. Abducted and killed last weekend, he will be buried tomorrow, not far from Jayapura's airport. He may be the first well-known "martyr" for the independence movement, but clearly tens of thousands, or maybe more, have preceded him.

In addition to the confirmed dead, the Paniai report lists another 13 people as missing, while 94 women and girls are listed as having been raped by Abri. Nearly all the rape victims were school students, seven of them at primary school. One of the girls, who was apparently "accused of being a child of the OPM" – the armed Free Papua Movement – is listed as less than five years old.

The vast majority of the dead were men. The dates of their deaths range from 1969 to 1998. Every one is listed as "shot dead" by Abri. Paniai and other highland regions have long been strongholds of the OPM.

Indonesia has held Irian Jaya since 1963. Researchers say there were particular upsurges in repression around 1969, when a UN-monitored "Act of Free Choice" was held among just over 1,000 tribal chiefs. This resulted in a decision to join Indonesia but was marred by widespread killings. Many of the dead in the Paniai report died in 1969.

A second round was in 1977, when there was an upsurge of activity by the OPM, encouraged by the independence of Papua New Guinea in 1975.

Els-Ham and other monitoring groups have passed the Paniai report on to other investigators, including Indonesia's National Human Rights Commission.

"They have a bitter experience. They felt that the issue of human rights was never settled by Indonesia. We reported to organisations that can help to solve the problem for the people," said Mr Renwarin.

So far, the follow-up has been minimal, as with a handful of other similar reports.