Resistance leaders in the restive Indonesian region of West Papua say they are losing their struggle for independence as authorities step up a decades-long campaign of abuse and intimidation.

After almost 50 years of Indonesian rule, the reins of control are being pulled tighter than ever, with human rights groups saying the frequency and ferocity of abuse is on the rise.

There are even claims that an elite counter-terrorism unit, one that has been funded and trained by Australia, is operating in West Papua where it is accused of targeting and killing independence leaders.

The ABC's Hayden Cooper went undercover in the secretive Indonesian provinces, where he discovered a police state operating with impunity.

The sheer scale of the police and military presence is obvious from the moment of arrival in the ruggedly beautiful region - a treasure trove of mineral wealth and a place where two vibrant cultures meet and struggle for the right to rule.

On Tuesday's 7.30, Hayden Cooper and Lisa Main ask if funding and training provided by Australia is being used to target Papuan independence leaders.

Police and military outposts dotting roads at almost every kilometre are augmented by an unmarked, plain-clothed brigade of motorbikes - many of them allegedly police - and a coordinated web of police informants.

Mostly Indonesians, the informants could be shop owners, taxi drivers, hotel workers who watch the independence groups and pass information back up the chain to police for money.

Andreas Harsono, from Human Rights Watch, says West Papuans live in a constant state of fear.

"The Papuan people live in fear, in a constant fear, because of how many human rights abuses they suffered over the past five decades," he said.

And the heavy security presence keeps the closest eye on the independence leaders, including Victor Yeimo, the chairman of the West Papua national committee (KNBP).

Speaking from a safe-house in the capital, Mr Yeimo told 7.30 his organisation was peaceful and simply pushing for a referendum on Papuan sovereignty.

"No we don't use violence. We believe that in the open era, we believe one of the best methods we have to use is civil power now," he said.

"I don't think about how Indonesian they will attack me or target me, I don't feel about that - I don't think about it. What I'm thinking is how I can bring my people to freedom."

Beatings and intimidation

Two cultures are struggling for the right to rule West Papua. ( ABC TV )

But the Indonesian security forces are determined to crush that struggle.

At the Papuan National Congress last October, Indonesian forces took the extraordinary step of opening fire on the gathering, killing three people.

Human rights activists say the security forces responsible for abuses like these included the elite counter-terrorism unit, Detachment 88, a unit funded and trained by Australia.

It is now operating in West Papua, where it is accused of targeting and killing independence leaders.

Violence like this stretches back to the 1960s, when the Dutch colonial rulers pulled out.

At the time Papuans faced a choice - independence or Indonesia - and amid widespread reports of beatings and intimidation, 1,000 elders specially selected by Jakarta voted for the latter.

To this day Papuans consider it a travesty, and they have fought to overturn it, with Amnesty International estimating that at least 100,000 Papuans have been killed since the 1960s.

Extra-judicial killings in Papua still happen frequently - in 2010 alone, the Asian Human Rights Commission reported a dozen cases, and video of torture and abuse at the hands of Indonesian forces is common.

Death toll

The death toll from the past three months alone speaks for itself, with five KNBP activists targetted and killed by police or military forces.

And just eight weeks ago the Indonesian army went on a violent rampage, attacking a town near Wamena in the country's Highlands.

"That day the army soldiers came and punished us," one witness said.

"I got beaten and had to have six stitches in my hand and also 20 stitches in my head.

"They beat me in the legs and now it is hard to walk. That's how they punished us."

The witnesses say 300 soldiers destroyed the village in retaliation for the death of one of their own, injuring dozens of villagers, killing one man and burning down 87 houses.

"My house was burnt down by the battalion and I have still haven't been compensated," another witness said.

"This house was built when I was a child. Now we are living in huts, in tents."

Struggle for freedom

Andreas Harsono sees it as an all-too-common example of the military acting without boundary.

"The army says they are investigating the soldiers," he said.

"But from what I know, the witnesses, survivors, the people whose houses were burnt, none of them, especially the prominent ones, the most articulate ones, none of them say they have ever been questioned by military police over the rampage.

"So these are things happening over and over again in Papua."

Despite the overwhelming odds, Mr Yeimo says he is determined to keep fighting, even if it means his name could soon be added to the list of the dead.

"That is the consequence of the struggle," he said.

"We know that we will die, we will shot by them.

"It's not a new thing, it's not a new story, we have been killed by them - many of our elder have already been killed by Indonesia.

"But we will struggle for freedom because if not me, who? There's no way - we will struggle, we will fight or we will be lost from this country.

"We know it."