Zack Schofield was one of six Australians detained by the Israeli military while attempting to transport aid to Gaza.
They were among 175 flotilla participants detained on Wednesday by the Israeli Defence Force out of nearly 700 heading across the Mediterranean.
Speaking to AAP from the Greek island of Crete on Saturday he said some people were shot at point-blank range with rubber bullets as soldiers boarded their boats in international waters.
"Some of us were kicked and punched as we were being processed on our own boats, many of which were sunk," Mr Schofield said.
The detainees were transferred to an Israeli prison ship which had containers on the deck to house them.
"We were dragged along the floor, forced to kneel with our heads touching the ground, some of us were dragged by our hair," Mr Schofield said.
Some were taken into a container and beaten with the butts of rifles and an American was kicked in the testicles and bashed in the head, he said,
"We could hear the beatings."
At one point the soldiers moved on the detainees with force, firing flash-bangs, one of which landed at his feet and exploded, Mr Schofield said.
The detainees were transferred to the Greek Coastguard, with many having to go straight to hospital.
"Compared to what Palestinians undergo in Israeli prisons ... we got off lightly," Mr Schofield said.
"The Israelis were doing everything they could to inspire terror in us."
The flotilla members were extremely concerned for two Palestinian leaders of the aid mission who were taken to Israel and were probably being tortured, Mr Schofield said
"We're demanding that Australia break its alliance with Israel ... because Israel is constantly breaking every international law in the book and conducts violence against international citizens with absolute impunity"
The activists were involved in a second Global Sumud Flotilla, attempting to break an Israeli naval blockade.
Mr Schofield, along with Australians Ethan Floyd and Neve O'Connor, sent a video message from Sitia in Crete, saying detainees had been harmed.
Israel's foreign affairs minister Gideon Sa'ar confirmed the vessels had been intercepted but insisted participants were not harmed.
Surya McEwen, Cameron Tribe and Bianca Webb-Pullman round out the six freed Australian detainees, among 17 known to have been participating in the flotilla.
Organisers claim the Israeli actions were unlawful as they occurred in international waters far from Gaza.
"This is piracy," the Global Sumud Flotilla said in a statement.
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.
"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.
Israel controls access to the Gaza strip and denies withholding supplies for region's two million residents.
The Department of Foreign Affairs and Trade said consular officials in Crete were providing assistance to Australians there as part of the flotilla.
"We understand people want to respond to the humanitarian situation in Gaza but we continue to urge Australians not to join others seeking to break the Israeli naval blockade as they will be putting themselves and others at risk of injury, death, arrest or deportation," it said in a statement.
