Pro-independence leaders in the Indonesian province of Papua want a limit on when the separatist symbol, the Morning Star flag, is flown this weekend.
It comes amid concerns that extreme militant groups may use the flying of the flag as an excuse for violence during Papua's 41st anniversary commemoration of its attempt to establish independence in 1961.
Willie Mandowen, from the Papua Council, says religious militants from other troubled provinces have arrived in Papua, and intend provoking violence.
He says any violence will give Indonesia's military an excuse to crackdown on the pro-independence groups.
Earlier, the Indonesian President Megawati Sukarnoputri, urged the separatists not to celebrate the anniversary and that measured action will be taken against those who do.
Mr Mandowen says to avoid possible violence, the Presidium Executive has instructed that the Morning Star not be flown with the exception of four in memory of the Papuan leader Theys Eluay who was murdered allegedly by members of the military a year ago.
"There will not be any flag raising but ceremonies will proceed. We know that there may be a third party, elements that used to play the game in East Timor and Maluku that can provocate the people to raise the flag and therefore it becomes a justification for the military and police to be more repressive."
Willie Mandowen, from the Papuan Council.
Yesterday 12 people were arrested in Manokwari, in Papua's west, for flying the Morning Star.