An Australian boat carrying pro-independence activists to Indonesian Papua will be turned around, the head of the military in the province's port city of Merauke says.

The so-called Freedom Flotilla was expected to cross into Indonesian waters on Thursday afternoon local time despite warnings from Jakarta as well as the Australian government that the activists should abandon their mission.

The commander of the Indonesian forces in Merauke, Brigadier General Edi Rahmayadi, on Thursday repeated previous warnings that the group would be turned around, saying there would be "no compromise".

"They cannot enter sovereign territory of our country as long as they don't have cleared document," Brig Gen Rahmayadi told AAP.

"They will not be taken to land. They will be expelled while they're on the sea."

"No compromise on that. They'll definitely not be taken to the land first."

The group is making the journey to support the struggle for Papuan independence from Indonesia and alleged violence by authorities.

The Freedom Flotilla was initially made up of three boats with about 20 Australians and West Papuans aboard, and set sail from Cairns last month bound for Papua.

But due to mechanical problems just six activists aboard one boat, the Pog, are sailing the final leg of the journey.

The group's spokeswoman Izzy Brown, who is on board the boat, says the Freedom Flotilla is a peaceful mission and the activists pose no threat.

None of those on board the Pog, including an Australian, a New Zealander, a Kenyan and a West Papuan, have permission to enter Indonesian waters.