Mark Dodd, Suai – When Detective Senior Sergeant Matt Reynolds took part in a recent murder case in Canberra, about 20 detectives were assigned within 24 hours to solve the killing.

Now based in south-west Suai, serving with the United Nations Civilian Police (Civpol), Sergeant Reynolds and an American colleague, Detective Dan Jankowski, are trying to solve up to 500 homicides and several hundred cases of rape.

The crimes were committed in Cova Lima district by pro-Jakarta militia and members of the Indonesian security forces in September after East Timor's vote for independence.

"We're looking at anywhere between 300 and 500 murder cases – 200 of these could be from the Suai Cathedral massacre," Sergeant Reynolds said. "We just won't know until we find the bodies."

Pointing to a crammed filing cabinet marked "Homicides", he said additional murder cases were piling up at the rate of between three and five a week. "I'm looking at dozens of murder cases at the moment – it's just beyond normal police experience. A lot of murder cases haven't been reported because we're having a hard time getting up into some areas.

"Separate from the church massacre there is a 14-person massacre site at Lactos," he said. Lactos is a small hamlet north-west of Suai in mountain country about 12 kilometres from the border.

Detective Jankowski, in charge of investigations in Suai, said: "We haven't had a chance to concentrate on the rapes – we're still trying to catch up with the murders."

He emptied a yellow envelope detailing the latest atrocity. "We've found a militia torture house at Beco, 10 kilometres east of here."

Locals say that for two weeks the former Indonesian government building held 27 men and one woman suspected of being independence activists.

Polaroid photos show what appears to be bloodstained walls, a club, manacles, and some graffiti including the words "I love you darling" scrawled on the wall. Empty shell casings at the site support claims that two people were murdered there.

However, it was the Suai Cathedral massacre on September 6 that galvanised international attention and remains one of the worst of the documented post-ballot atrocities.

In a four-hour killing frenzy supported by Indonesian troops, militia armed with automatic weapons, clubs, machetes and hand grenades rampaged through the cathedral grounds, killing suspected independence activists and their supporters.

Civpol investigators believe at least 100 people were killed, but that figure is a conservative estimate and at odds with claims by locals.

Both Civpol investigators said they had strong evidence linking known militia leaders to the crimes. "We've identified suspects in about two-thirds of the cases," Sergeant Reynolds said. "The problem is getting them out of [Indonesian] West Timor.'

Heading the list of suspects is Ezieo Maneh, a Laksur militia commander who has a penchant for changing his name. A Mahidi commander, Antoine Lemos, who tried to sneak back into East Timor, was arrested in nearby Zumulai on charges of murder and is being held in the UN detention centre in Dili.