The Free West Papua Campaign says West Papuan refugees living in Vanimo in Papua New Guinea fear they will be killed in revenge for the armed clashes on the Wutung border post.
A number of separatist rebels from Papua's OPM have reportedly crossed from Indonesia since the clash.
The Campaign's founder Benny Wenda says the refugees believe if PNG police fail to find the rebels then Indonesia will force them to arrest West Papuan refugees near the border.
He says the refugees have told him they live in fear.
"Because they have experienced when the Indonesian military couldn't find the freedom fighters because they run to the bush. And then they use Papua New Guinea police to look into Papua New Guinea. (if) they couldn't find them sometimes they also burn their houses because they're angry. The refugees who contacted me, they told me - if they couldn't find these freedom fighters, they will turn to us."
Benny Wenda, Founder of the Free West Papuan Campaign who is in exile in Britain.