Indonesian authorities have warned Australian activists on a "freedom flotilla" to avoid entering West Papua or risk being arrested.
The Associated Press reports Indonesia's President Susilo Bambang Yudhoyono urged friendly countries to intervene to prevent damaging diplomatic relations.
In his Independence Day speech to parliament, Mr Yudhoyono said "Do not hurt the feeling of Indonesia because we do not want to hurt (others)."
A flotilla of at least two yachts will soon set sail from Cairns up the coast of Cape York and across the Torres Strait to Daru Island, in southern Papua New Guinea, from where they plan to sail onto the Indonesian-controlled territory of West Papua.
A reported group of 30 Australian Aboriginal, non-Indigenous and West Papuan activists have volunteered to take turns crewing the yachts.
Free Papua activists say the aim of the voyage is to draw world attention to "ongoing atrocities" by Indonesian security forces.
But the Freedom Flotilla may be turned back as they don't have permission to visit Indonesia.