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The ABC has obtained exclusive video which reportedly shows the aftermath of a deadly crackdown by Indonesian troops who attacked an independence rally in the restive province of West Papua.

Six people died and many more were injured after troops and police broke up the meeting of the Third Papuan People's Congress in the province's capital Jayapura on October 19.

Security forces moved in after the meeting, which was attended by thousands of people, declared independence from Jakarta and decided to elect its own government.

Among the forces involved in breaking up the meeting were Australian-trained elite anti-terrorist troops.

ABC1's Lateline has obtained exclusive pictures claiming to be of the aftermath of the rally, which show a car covered in bullet holes and motorbikes and scooters abandoned by the side of the road.

The Indonesian government says police fired warning shots to disperse the crowd and made many arrests.

But six people were found dead after the rally, reportedly from bullet wounds, and six more have been charged with treason.

The Indonesian government says there were deaths, but not at the site of the Congress, and says the victims' wounds were not gunshot wounds, but were caused by a sharp weapon.

Those who witnessed the violence want the international community to intervene.

I call on the churches around the world to care about this... we are now in a dangerous situation and we're calling for a UN intervention to help us.

Protestant minister John Baransano John Baransano, a Protestant minister in Jayapura who was at the rally, says international help is needed.

"I call on the churches around the world to care about this. I'm calling for an intervention for us because today's events show that we need a transitional government and this needs to happen to help the people of Papua," he said.

"We are now in a dangerous situation and we're calling for a UN intervention to help us."

He said he saw people being shot and beaten and others herded into trucks.

"I saw with my own eyes people who were bleeding. They had been hit. We saw how they were terribly harassed," he said.

"They were forced into a truck and ordered to sit down so they wouldn't be seen by others. But if we were up higher, we could see what had been done to them."

images:http://www.abc.net.au/news/image/3581262-3x2-940x627.jpg

Anglican minister Peter Woods lived in Indonesia for many years and is dedicated to helping West Papuans achieve independence.

He was in Jayapura during the Congress and filmed interviews with many of the independence movement's leaders.

He said the security forces waited until independence was declared at the meeting.

"The army, the special police, the Brimob [Mobile Brigade], the Densus 88, which had been along the road for the last three days in various barracks and positioning areas, they all moved in and started firing," he said.

The Densus 88 unit is Indonesia's elite anti-terror squad and is funded and trained by Australia and the United States.

The Australian Government says the training for the Indonesian armed forces emphasises human rights awareness, accountability and respect for the rule of law, including in Papua, and that it does not train Indonesia's military to counter separatist groups.

But Greens Senator Richard Di Natale wants military training halted.

"The Australian Government should immediately suspend all support for the Indonesian military. It should, as a matter of urgency, send a fact-finding mission to the region," he said.

Reverend Woods believes the violence on October 19 was premeditated.

"It was very well planned and they waited until the declaration had been made," he said.

Elite police from Jakarta and Indonesia's National Commission for Human Rights are investigating the shootings, but there are claims that some of the injured are too afraid to seek treatment for fear they will be arrested.

One of those is Abraham Kereni, who was a representative at the Congress.

"Then those - the security forces, they immediately held pistols and opened the door of the car of the prime minister," he said.

"It was there that shots were fired. They opened the door and pulled me out. As they were pulling me out, there were three crew that came and hit me."

A spokesman for Australia's Department of Foreign Affairs says it appears from reports that the police's response to the meeting was disproportionate.