Indonesian authorities have warned Australian activists on a "freedom flotilla" to avoid entering West Papua or risk being arrested.

In his Independence Day speech to parliament yesterday, Indonesia's President urged friendly countries to intervene to prevent political activities that could damage diplomatic relations.

"Through this confirmation (of mutual respect for sovereignty) I hope that all parties can be actively worked to prevent political activities that can disturb good relationships between Indonesia and other friendly countries," Susilo Bambang Yudhoyono told the national parliament.

"Do not hurt the feeling of Indonesia because we do not want to hurt (others)."

A flotilla of at least two yachts will set sail from Cairns tomorrow 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. Many are travelling on Aboriginal and West Papua passports which aren't formally recognised.

Senior Indonesian police officer Paulus Waterpauw says any Papuan activist aboard the flotilla who has a "previous criminal record" or is on "the wanted list" will be arrested on arrival.

But activist Amos Wainggai says he remains optimistic the flotilla will be able to enter West Papua. "I hope and I believe that we will be welcomed," he said.

Seven years ago, the 41-year-old and 40 others sailed from West Papua to Cape York where they sought asylum.

"When I was in West Papua I was part of a group that wanted independence," Mr Wainggai, who is now an Australian citizen, said.

"The military found out and then they started looking for me and my friends. If they found me I would have been killed."

Indonesia has been accused of using violence against West Papuans who have sought self-determination.

Mr Wainggai says he knows a number of people who have been killed in his homeland. He hopes West Papua will one day be "free" so that he can live there with his family once again.

"I miss everything, I miss my friends and family," he said. "I want to tell all Australians that we are human beings and we have to look after each other."

The Freedom Flotilla group travelled overland from Lake Eyre to Cairns earlier this month, stopping at Aboriginal communities along the way. A spokeswoman said the group will continue to request permission from Indonesian authorities to visit West Papua.

West Papua came under Indonesian control after a UN-brokered "act of free choice" in 1969.