Karen Polglaze, Dili – Bony arms raise gnarled hands in a shaky Mexican wave as the call to salute rings out across the buckled, weed-infested square of the village of Maubara.

About 250 men, some old and bent from years of subsistence farming, many young and angry after growing up in a region plagued by warfare, present their home-made guns, bows and arrows, spears and machetes as they are inducted into the troops of Besi Merah Putih.

Besi Merah Putih is one of around a dozen pro-integration paramilitary groups that have sprung up in troubled East Timor in the two months since the Indonesian government announced it might allow the province to secede.

Dressed in their usual garb of sarongs and thongs – or jeans and t-shirts for the younger members – this band of fighters hardly seem to live up to the strength of their name: Red and White Iron (a reference to colours of the Indonesian flag).

But from a distance their matte-black wooden arrow-shooters look like the real guns their leaders admit to having and using, and their existence has added a new layer of fear to the lives of the tens of thousands of people who live in fragile palm hut villages scattered across the territory.

Paramilitary groups like Besi Merah Putih have claimed responsibility for attacks on villages that have left scores of people dead and injured and have forced hundreds of people to flee to the safety of churches and houses outside their districts.

Although the highways around Maubara, about 50km west of Dili, are now free of the road blocks used by the paramilitary groups to terrorise the hundreds of people flocking to the town's relative refuge, people are still too scared to return home.

Despite their appearance as a rag-tag force, these alternative armies have some powerful backers. The Indonesian military (ABRI) officers have admitted arming the paramilitary groups to carry on their fight.

ABRI usually keeps a tight control on the population in an effort to defeat the Falintil armed resistance that has been fighting the military since the Indonesian invasion of 1975.

But at the Maubara Besi Merah Putih induction, ABRI officers and police could be seen watching benignly as the district regent, Lioneto Martins, inspected the troops of what amounts to an alternative military, an unthinkable creation anywhere else in the archipelago.

"We must live or die for the red and white [Indonesian flag]," Lioneto told the troops. "Many people died in the civil war. Now we want peace, not a civil war."

The creation of the paramilitaries has fuelled fears that civil war will erupt should Indonesia pull out of East Timor in the same way that former colonial power Portugal did in 1975. But those fears were a myth spread by Indonesia to justify its harsh military regime, according to the resistance movement.

National Council of the Timorese Resistance (CNRT) spokesman David Ximenes told AAP that it was only since the paramilitary groups were formed that new conflicts erupted across the half-island.

"Indonesia always claimed that if you let East Timor be free, East Timor will come up with a new civil war," said Ximenes who was imprisoned for his political beliefs by the Suharto regime and freed by the retired general's successor, President BJ Habibie. "But actually, Indonesia is the protagonist."

Many in East Timor share that opinion, but no-one has an explanation as to why Indonesia, which seems to have washed its hands of the troublesome province, would bother trying to recreate the situation it used as an excuse to invade the territory in the first place.

Most settle on face-saving on the government's part, or believe that it is ABRI acting on its own to exact revenge for the lives lost in the ultimately hopeless Timor conflict, Ximenes said.

Ximenes is counting on the UN to send peacekeepers to enforce a peace that does not yet exist. He believes the force will be sent should the Indonesian military pull out.

For now it seems the shadowy paramilitary groups such as Besi Merah Putih are the more pressing problem. They too must lay down their weapons if some kind of peace is to be brought to an emerging independent or autonomous East Timor. But for ordinary people it matters little who's carrying the guns. The bullets kill all the same.