The flotilla once had three boats, but is now down to one, the Pog, which carries just six people, after other boats broke down and could not be repaired.

None of the indigenous Australian protesters who have travelled with the flotilla remain aboard, and Amos Wanggai, who fled Indonesia’s restive province in 2006 and was granted refugee status in Australia, is the only West Papuan.

Flotilla leader Jacob Rumbiak is “still on Thursday Island and is available for talking and negotiating with the Indonesian military'', a spokesman said.

Earlier plans to stop off in Papua New Guinea have also been abandoned due to a threat from local police to arrest them.

The Pog is expected to take two to five days to reach West Papua.

But Indonesian navy spokesman Untung Surapati said armed forces headquarters in Jakarta had issued an instruction: “Don’t let the Freedom Flotilla enter Indonesia.''

“So as long as the order still stands, we keep our alertness high,” he said.

Captain Goeroeh Ardianto, an Indonesian navy spokesman at Merauke, West Papua, where the boat is heading, said if the protesters were armed “we have to be extra careful in handling them”. “But if they are not, we’ll try to have some dialogue with them. If they insist on illegally crossing the maritime border and we are forced to take strong action, we will.”

The navy had not beefed up its forces, and only its normal sea patrol was operating in the area, Captain Ardianto said. This includes the KRI Mulga warship and three small patrol boats.

A troop carrier with about 1500 soldiers landed in Merauke in late August, prompting fears from the protesters that troops were reinforcements sent to intercept them. But Captain Ardianto said it was just the normal rotation of troops to the area being replaced.

The expedition is designed to highlight the suppression of political rights in West Papua and to express solidarity between the indigenous people of Australia and West Papua.

Despite comments from outgoing foreign minister Bob Carr that the protesters would receive no consular assistance at all, the Australian Foreign Affairs ministry has offered normal consular help if they are arrested in Indonesia.

Coalition foreign affairs spokeswoman Julie Bishop said Indonesia is entitled to use “whatever means it wishes to protect” its territorial integrity, and that  “Indonesia is within its rights to turn these boats around where it is safe to do so''.