Human rights groups have called for Australian monitors to be allowed into Papua amid reports people are fleeing parts of the Indonesian province due to fears of another violent crackdown on pro-independence rallies planned for next week.
However, the Indonesian government considers the raising of the flag an act of treason.
At least three protesters were killed and another 90 people injured last month when Indonesian police and military stormed a pro-independence rally in Abepura after the raising of the Morning Star flag.
Video of the aftermath of the rally, broadcast on Australian television, also showed police beating unarmed protesters, including children.
As many as 300 people were arrested.
A spokesman for the pro-independence group, the National Committee for West Papua
(KNPB), has told AAP that large numbers of people have begun leaving Jayapura and Manokwari in Papua, fearing a backlash from security forces at rallies planned for Thursday.
As Indonesia remains off limits to foreign journalists, the report could not be confirmed.
In the letter to Mr Rudd, Human Rights Watch and the Human Rights Law Centre raise concerns about the likelihood of a repeat of last month’s violence as well as the use of excessive force by the police and military.
The letter calls on Mr Rudd to urge the Indonesian government to allow full and free access of journalists to Papua and to deploy Australian embassy staff to monitor and observe events on December 1.
The human rights organisations say there should also be a full and impartial investigation into the deaths and injuries, and allegations of excessive use of force by the authorities, arising from the demonstration in Abepura on October 19.
But the letter also criticises the Australian Ambassador to Indonesia Greg Moriarty who had described the actions of the protesters at the rally as provocative.
“In our view, a clear and firm public statement on Australia’s position on human rights in the area is critical, especially since there is a real risk that Australian Ambassador Greg Moriarty’s recent reference to the actions of Papuan People’s Congress leaders as illegal, provocative and counterproductive may otherwise be interpreted as supporting a government crackdown on the congress,” the letter said.
Mr Moriarty, however, had also pointed to the response by Indonesian security forces as being disproportionate.
The letter to Mr Rudd also questions Australia’s funding and training of Indonesia’s elite anti-terrorism squad Densus 88
, members of which were among the security forces present at the rally on October 19.
“Australia plays a critical leadership role on human rights in Asia and the Pacific and should take a principled and proactive stand on human rights with a key partner like Indonesia,” the two human rights organisations said.
Indonesia has been battling a long-running but low-level insurgency since its takeover of Papua in 1969.
However, the security situation has deteriorated in recent months with the province experiencing its worst violence in years.
Figures from Indonesia’s Commission for Missing Persons and Victims of Violence show at least 40 people have been killed as a result of the violence since the beginning of July.