The activists were among more than a hundred people involved in a second Global Sumud Flotilla, attempting to break an Israeli naval blockade.
They were released on Crete after being intercepted off the coast of the Greek island by the Israel Defence Forces on Wednesday.
Organisers of the flotilla said three Australians, Ethan Floyd, Zack Schofield and Neve O'Connor, were taken to hospital for injuries after being released.
They say they were subjected to violence and mistreated on board the Israeli vessel.
"We three are all physically OK as you can be after that experience," the trio said in a video message from Sitia hospital in Crete.
All 173 international activists were released except for two leaders of the flotilla, Thiago Ávila from Brazil, and Saif Abu Keshek from Spain, organisers said.
Mr Floyd, Mr Schofield and Ms O'Connor said they would hunger strike until the health and whereabouts of the remaining detainees was confirmed.
Israel's foreign affairs minister Gideon Sa'ar confirmed the vessels had been intercepted but insisted participants were unharmed.
'All participants in the provocative flotilla who were taken off the vessels were taken off unharmed," he said on X.
The vessels were seized in international waters off Greece's Peloponnese peninsula, hundreds of kilometres from Gaza, organisers said.
Surya McEwen, Cameron Tribe and Bianca Webb-Pullman round out the six Australian detainees, among 17 known to have been participating in the flotilla.
Organisers claim the IDF's actions were unlawful as they occurred in international waters far from Gaza.
"This is piracy," the Global Sumud Flotilla said in a statement.
"This is the unlawful seizure of human beings on the open sea near Crete, an assertion that Israel can operate with total impunity, far beyond its own borders, with no consequences."
Israel's Ministry of Foreign Affairs said the two remaining detainees had been brought to Israel for questioning.
"Saif Abu Keshek, suspected of affiliation with a terrorist organisation and Thiago Ávila suspected of illegal activity, will be brought to Israel for questioning," it said on X.
Organisers called for their immediate release.
"We demand that all governments do all they can to pressure the Israeli regime to release all the illegal abductees," the Global Sumud Flotilla said.
Seven Australians were detained by the IDF during the previous Sumud flotilla in October.
Israel controls access to the Gaza strip and denies withholding supplies for regions two million residents.
But Palestinian and international aid bodies claim supplies to the territory are insufficient despite guarantees of increased aid.
The Department of Foreign Affairs and Trade, which has been contacted, has previously urged Australians not to participate in breaches of Israel's blockade.
Sydneysiders are set to paddle across Sydney Harbour on Sunday to show support for the flotilla.
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