The Pacific Conference of Churches claims Fiji police tried to seize a West Papuan independence flag.
The Christian church group raised the Morning Star flag on Tuesday to protest the killing of Papuan demonstrators during unrest in Indonesia.
It said three police officers then visited its secretariat in Suva and warned the flag breached Fiji's Public Order Act.
Police seized a Morning Star flag from the same property in 2014 and never returned it or laid charges, the group said.
Fiji police did not respond to requests for comment.