Independent senator Nick Xenophon says West Papuan activists were "effectively threatened" to leave the Australian consulate in Bali ahead of Prime Minister Tony Abbott's arrival for the APEC summit.
Senator Xenophon is demanding an immediate explanation for the departure of the three men, after they scaled a wall into the mission early on Sunday morning.
He alerted AAP to the incident after being contacted by human rights groups.
It's understood Australian officials persuaded the trio - Rofinus Yanggam, Markus Jerewon and Yuvensius Goo - to leave the consulate about 7am local time.
The three men were calling for international journalists to be allowed into the troubled Papuan provinces and for the release of at least 55 political prisoners from Indonesian jails, including Filep Karma, who has been jailed for 15 years in Abepura prison.
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The security breach came ahead of Mr Abbott's arrival for the APEC leaders' summit on Sunday.
Senator Xenophon called on Australian Foreign Minister Julie Bishop to provide a detailed timeline and explanation of what occurred.
"These three young men were not asking for West Papuan independence from Indonesia. All they were asking for is entirely consistent with the Lombok Treaty of 2006, signed by both Australia and Indonesia," he said.
"Instead of getting sanctuary and help, the Australian government effectively threatened them and now there is serious concern over the activists' safety."
Senator Xenophon's calls were backed by Professor Clinton Fernandes of the University of NSW, who has written extensively on West Papua and the Australian/Indonesian relationship.
He said when the media circus had moved on after APEC, the trio "may be tried, most certainly they will be beaten, and at some point might be disappeared".
Mr Yanggam told the Guardian Australia he left the consulate in fear for his life after the consul-general, Brett Farmer, told them the Indonesian police and army would be called.
"They told us: '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 said.
"I know that if I am arrested then my life will be over. So better to get out now."
In a letter addressed to the Australian people, the trio said they wanted Mr Abbott, Japanese Prime Minister Shinzo Abe and US Secretary of State John Kerry to stand up for Papuan rights.
"We want these leaders to persuade the Indonesian government to treat Papuan people better," the handwritten letter said.
Many of their colleagues had tried to have their voices heard but had ended up in prison, they said.
"These political prisoners committed no crime. They are explicitly committed to non-violence," the letter said.
"The Indonesian government arrested and jailed them for discussing their political human rights beliefs."
The trio ended the letter with a plea for help.
"We seek refuge and plead for our safety."
Australia's Department of Foreign Affairs and Trade said the trio had left the consulate "voluntarily" at 7am Bali time after delivering a protest letter.
Interim Labor leader Chris Bowen said he had full confidence that the consul-general and Australian officials were acting appropriately.
