Local activists have challenged the authorities' version of events - that police and soldiers fired into the air, when the third Papua People's Congress tried to raise the Morning Star flag, and to proclaim the state of West Papua.
Ferry Marisan is director of the Institute of Human Rights Study and Advocacy in Jayapura. He's interviewed eye witnesses who saw meeting participants being shot.
He says many Papuan Congress participants are still hiding from police.
Presenter: Sen Lam
Speaker: Ferry Marisan, director of the Institute of Human Rights Study and Advocacy in Papua
MARISAN: The situation in Jayapura today will be ok now, but for people in West Papua, who were involved in the West Papuan Congress are still afraid. They came from all regencies in Papua and they stayed in the dormitories and stayed with their families here. And they're still afraid that the intelligence (service) will send messages by mobile phone and the police will come to the dormitories and then look for people who were involved in the West Papuan Congress.
LAM: Reports from Jakarta are speaking of one fatality from yesterday's Papua Congress meeting in Jayapura - what can you tell us about that?
MARISAN: Not one person.. I think six persons. Yesterday they killed six persons, because this morning, we found two bodies. One of the students in university - his name is Daniel Kadepa, and yes, six people. So, they already found two bodies. They were killed by TNI (Indonesia's military) around 100 metres from the area of the Congress and then this morning, already taken by police and TNI troops and they took the two bodies to hospital, to the local hospital, for an autopsy.
LAM: How do you know the people were killed by the TNI.. what sort of injuries did they have?
MARISAN: Well, I'm .. I interviewed a woman who witnessed the shooting by TNI. Daniel was dead in front of witnesses, so I just interviewed her.
LAM: Papua's military commander, Major-General Erfi Triassunu said that the troops only fired warning shots, and not at people. But obviously, you've heard differently?
MARISAN: The six people shot by the TNI were already dead, and now, I received information from one village very far from Jayapura, around 48 kilometres. They just called me, asking me to send my staff to investigate there, because the Papuans last night brought four people, brought them and put them in one village, and they need assistance from my staff, to take information. The name of the village is Sabron Yaru.
LAM: And do you intend to give this information to the local authorities, for them to conduct investigations?
MARISAN: Well, I will send my staff to that place, to get the information and I will send it to local authorities here also and to the police here.
LAM: How many people are in police detention, as far as you know?
MARISAN: In police detention right now, sixteen.
LAM: Sixteen people have been detained by police?
MARISAN: Yes, and their lawyer, he was in the local police and he's collecting information.
LAM: Do you think there's likely to be more arrests?
MARISAN: I think so, because the local commander of police in Jayapura is still looking for the head of the committee of the Congress. Now they're still looking for him, and then maybe they will also look for other heads of delegation for the Congress.
LAM: So are there people in hiding, as we speak?
LAM: People are hiding from the police?