It appeared we were being followed.

Several times during the day, our driver noticed different motorbikes or vehicles apparently tailing our car from a distance.

We had been warned this would happen.

Before coming to Sorong, we were told we would almost certainly be under surveillance by Indonesian military intelligence personnel.

It is rare for foreign media to be allowed into either of Indonesia's two restive Papuan provinces, especially at such a volatile time, with sporadic protests and riots continuing across the region.

The ABC was able to shake off the vehicles which appeared to be following it before meeting with Yosina. ( ABC News: Phil Hemingway )

And we were there to meet 27-year-old activist Yosina.

Yosina (not her real name) has gone into hiding since she took part in pro-independence protests that erupted into violence last month at Sorong, the biggest city in West Papua province.

She now lives in fear of being kidnapped or killed by Indonesian authorities.

Before agreeing to meet the ABC for an interview, she went to lengths to avoid being seen or captured.

Yosina said activists were fighting "the occupation of Papuan land". ( ABC News: Phil Hemingway )

She waited until we pulled up at a small hotel in Sorong and watched from a window to see if we had been followed.

But, coming to a halt, we appeared to have shaken off any vehicles on our tail.

With the all-clear, Yosina came out to greet us, her head covered by a hoodie.

Yosina has gone into hiding since taking part in pro-independence protests. ( ABC News: Phil Hemingway )

She then jumped on a motorbike with a friend to lead us through back streets to a rundown house on the edge of town.

Inside, she told us on camera — with her face just a silhouette — about the reprisals she and other activists fear in the wake of last month's protests.

'What we're fighting is the occupation of Papuan land'

It is rare for foreign media to be allowed into either of Indonesia's two Papuan provinces. ( ABC News: Phil Hemingway )

The protests at Sorong and other key Papuan centres were triggered by perceived racist comments made by Indonesian police towards Papuan students in Java the weekend before.

But the racist insults were the fuse that ignited Papuans' deeper anger at Indonesian repression, amid a decades-long campaign for Papuan independence.

Hundreds of pro-independence protesters at Sorong torched buildings, smashed windows and blocked roads with burning tyres.

Hundreds of prisoners escaped after setting the jail alight.

This West Papuan prison was set alight during recent protests. ( ABC News: Phil Hemingway )

Fifteen activists were arrested and detained for hours, Yosina tells us, accused of being "provocateurs". One protester evaded capture but was beaten on the face, leaving his eyes bloodied and bruised.

"We are fearful, not only activists but all Papuans," she said.

"Because we're outnumbered. There are so many non-native Papuans here.

"We can't sleep at night.

"When we're lying down, we hear the sound of planes and choppers like they are about to land, that makes us feel threatened."

Police tape still surrounds the fire-damaged West Papuan jail where hundreds of prisoners escaped. ( ABC News: Phil Hemingway )

But Yosina said no amount of fear would stop the Papuans' fight for independence from Indonesia.

"It goes beyond racism. Papua is being occupied. We want to determine our own fate," she said.

"What we're fighting is injustice, and the occupation of Papuan land.

"Papua's independence is the ultimate resolution."

Police reject suggestions activists harmed

Sorong, the biggest city in West Papua province, erupted in violence last month. ( ABC News: Phil Hemingway )

A wave of similar protests has erupted across both provinces since August 19, representing the worst civil unrest in Papua for years.

Last week up to six protesters were shot dead at Deiyai in neighbouring Papua province, when Indonesian police fired into a crowd of protesters.

In the past fortnight Indonesia has sent thousands of extra security forces into both Papua and West Papua provinces, to try to quell the ongoing unrest.

Police say they have regained control in West Papua. ( ABC News: Phil Hemingway )

At Sorong the ABC observed about 500 riot police from the "Brimob" unit (Mobile Brigade) who assembled along the main road in front of police headquarters before marching to their armoured vehicles to patrol the town.

Sorong's Police Commissioner Mario Siregar denies authorities hurt anyone in the recent riots, and says the city has now returned to normal.

"Until today no one is harmed and we don't want there to be any victims because we have orders from the national police chief and the TNI (armed forces) chief that we must operate in a humane way," he said.

"We have strict orders not to use live ammunition.

"I tell my officers every morning it's forbidden to use live bullets."

Commissioner Siregar also denied there was any prohibition on pro-independence protests, as long as organisers "follow rules" and do not allow weapons or disturb public order.

Indonesian security forces have descended on both Papua and West Papua provinces. ( ABC News: Phil Hemingway )

His comments directly contradict a national ban, announced earlier this week, on all demonstrations or speeches that promote separatism in Papua.

Indonesia's chief security minister Wiranto announced violators would face strict action and law enforcement, including criminal charges.

UN urged to 'correct history'

One indigenous leader in Sorong says all Papuans should be free to express their rights, including the right to a second referendum on independence from Indonesia, as the Dutch had pledged when they relinquished control of Papua in the 1960s.

The first referendum — in 1969 — was widely seen as a sham, because only a fraction of Papuans were allowed to vote, "under intimidation".

Silas Kalami criticised the UN for not allowing all Papuans to vote in the 1969 independence referendum. ( ABC News: Phil Hemingway )

"It wasn't one man-one vote, but one tribal leader represented many people, the whole tribe," Silas Kalami, a leader of Sorong's local Malemoi tribe, said.

"Before the Dutch left Papua, they formed the country of Papua. We had the flag, the currency. After that, the Dutch left and Indonesia was in.

"Papuans want their rights back."

Most West Papuans want independence, Silas Kalami says, but he acknowledges some would support greater autonomy within Indonesia. ( ABC News: Phil Hemingway )

Mr Kalami blames the United Nations for Papua's fate, for not allowing all Papuans to vote in the 1969 referendum.

"The UN should correct history … because it's their fault," he said.

"The UN must correct the 1969 referendum that was not done in accordance with proper UN procedures. It should have been one man-one vote, but it was done collectively and under intimidation."

Mr Kalami acknowledges some Papuans would support greater autonomy within Indonesia, rather than independence.

Silas Kalami says "Papuans want their rights back". ( ABC News: Phil Hemingway )

UN raises concerns

The UN yesterday expressed concern at the latest violence in Papua, including reports that pro-Indonesian militia groups had been involved in clashes with Papuan protesters. But it made no comment on Papuan calls for a new UN-sponsored referendum.

"We have been discussing our concerns with the Indonesian authorities," UN High Commissioner for Human Rights Michelle Bachelet said.

"There should be no place for such violence in a democratic and diverse Indonesia, and I encourage the authorities to engage in dialogue with the people of Papua and West Papua on their aspirations and concerns."

A UN delegation has sought Indonesian permission to visit Papua in the next few months, but so far no date has been set.