Indonesia has said ties with Australia could be strained if Canberra offers asylum to boat people claiming rights abuses in the province of Papua.
A government spokesman said the move "could disturb bilateral relations".
He was speaking two days after 43 people from Indonesia's eastern Papua province, including several children, reached northern Australia on a canoe.
Papua has been home to an ongoing separatist struggle since Indonesia took over in the 1960s.
Indonesian Foreign Ministry spokesman Yuri Thamrin said on Friday that Australia risked attracting a wave of boat people from Papua if it granted asylum to the 43 people.
Mr Thamrin also said that accepting their claims of abuses "could strengthen perceptions in Indonesia that there are parties in and around (Australia) who support or express sympathy for separatism".
The Papuans - who reportedly include leading pro-independence activists - arrived on Australia's northernmost Cape York Peninsula on Wednesday.
The group was reported to be carrying a banner that accused Indonesia of genocide in Papua.
Indonesia gained sovereignty over Papua - a former Dutch colony - in 1969.