Prime Minister Tony Abbott has reiterated his support for Indonesia's sovereignty over Papua while insisting three activists who breached the walls of the Australian consulate in Bali left the compound voluntarily.
The three men - Rofinus Yanggam, Markus Jerewon, and Yuvensius Goo - climbed the walls of the consulate in the early hours of Sunday morning to highlight claims of abuse and ill-treatment of West Papuans in the restive Indonesian province.
The men, who hoped to gain the attention of world leaders in Bali for the APEC summit, left the compound before 7am but it has since been alleged they were threatened with arrest by Australian Consul-General Brett Farmer.
Mr Abbott on Monday insisted the activists left of their own accord after a "lengthy discussion" and warned Australia would not be party to protests aimed at undermining Indonesia's authority over West Papua.
"We have a very strong relationship with Indonesia and we are not going to give people a platform to grandstand against Indonesia," he told reporters on the sidelines of the APEC summit.
"And people seeking to grandstand against Indonesia, please, don't look to do it in Australia. You are not welcome."
Mr Yanggam claimed consular officials threatened to call the Indonesian military unless the trio of protesters left.
"We don't accept you to stay here. If you stay here for five minutes, I will call the Indonesian army to come and take you out", Mr Yanggam quoted Australian officials as saying.
Australian Greens Senator Richard Di Natale said the three "effectively had a gun to their head".
"After hearing directly from the West Papuans involved, we now know the truth is that they only (left) after being threatened with being handed over to the Indonesian police," he said in Melbourne on Monday.
Senator Di Natale, the founding co-chair of the Parliamentary Friends of West Papua group, said West Papuan protesters would face imprisonment if handed over to the Indonesian authorities.
Indonesia, which took control of Papua from the Dutch in 1963, has for a long time fought a separatist movement in the province and faced various allegations of systematic abuse of the native population.
There have been numerous incidents of torture committed by the Indonesian military while the local population also complains that much of the wealth generated in the resource-rich province flows back to Jakarta while West Papuans remain poor.
Mr Abbott says the "situation in West Papua is getting better not worse".
"I want to acknowledge the work that President (Susilo Bambang) Yudhoyono has done to provide greater autonomy, to provide a better level of government services and ultimately a better life for the people of West Papua," he said.
The protest had threatened to overshadow what was Mr Abbott's first involvement in a meeting of world leaders since he was elected prime minister last month.
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