Indonesia says the activities of Australian-based Papuan pro-separatist groups are hampering its relationship with Canberra.
During a visit by Australia's Prime Minister, John Howard, the Indonesian security minister said the political activity in Australia provided an opportunity for activities that could disturb Jakarta's sovereignty in Papua.
The security minister said he understood that Canberra could not suppress freedom of speech.
But he argued that it was a different matter when political activity supported a push for independence.
The two countries have agreed to hold ministerial-level talks on the issue.