SAM IKIN | SBS World News
Foreign minister Marty Natalegawa said, after discussions with Australia and Papua New Guinea, all three countries are in agreement.
"Indonesia, Australia and PNG are all on the same page in not wanting such a stunt to interrupt or disrupt our relations," Mr Natalegawa says.
Two yachts set sail yesterday with about 30 crew members.
They were warned that if they enter West Papua waters they will be intercepted by Indonesian Navy vessels.
But the activists say they are highlighting abuses that West Papuans endure under Indonesian rule.
"That is something that you cannot turn a blind eye to when you hear some of the thing that are happening," says Natalia Papa.
Australia recognises West Papua as part of Indonesia but not all politicians do.
Liberal MP Warren Entsch says he supports the flotilla.
"I'm hoping at some stage that common sense will prevail and we'll be able to see West Papua regain its identity. Its true identity," says Mr Entsch.
One of West Papua's political leaders - who lives in Australia in self-imposed exile - says Australia needs to take a leadership role is helping bring about self-determination.
"We hope Australian government can be a third party to bring Indonesia and West Papua to sit together to talk about our future," said West Papua political leaders Jacob Rumbiak.
The flotilla is expected to reach West Papua in 12 days.
Meanwhile Australian foreign minister Bob Carr has warned protesters that they face up to five years' jail under Indonesian law.
Speaking from Jakarta, Senator Carr saids if they are arrested Australia can only offer consular support.
"If they're found to have committed offences under Indonesia's immigration law for not having a visa or permit or under Indonesia's anti-subversion law there is nothing that we can do to fight their case for them in Indonesian courts," he said.
"I want them to understand that very clearly before they get themselves into trouble."