Eleven Australians were among 400 people detained by Israel last week in international waters west of Cyprus.
The broader group of flotilla participants allege they suffered abuse at the hands of Israeli forces, such as broken limbs, sexual assaults, tasers to the face and being injected with unknown substances.
Seven of the Australian contingent arrived in Sydney on Monday morning, while the rest were due to arrive in Melbourne and Brisbane.
Walking out into the Sydney Airport departures hall, the Sydney flotilla participants returned triumphant with fists and peace signs held high.
A large contingent of supporters, including family, friends and federal senators greeted them on arrival with rapturous applause and chants of "free, free Palestine".
Flotilla member Surya McEwen ran into his mother's arms, while fellow member Zach Schofield embraced his parents and partner.
This was the third attempt by Mr McEwen, a dual diagnosis care worker from Mullumbimby, to deliver aid to Gaza via a flotilla.
During his most recent detention, he was held for 80 hours and alleges he was beaten in a room while Israeli soldiers sang the national anthem.
Mr McEwen likened the prison ships used by Israel to prisoner of war camps with nowhere to sleep, few toilets and platforms from which soldiers indiscriminately fired rubber bullets.
"We're all very tired, battered and bruised," he told AAP during a stopover before arriving in Sydney.
"While I was imprisoned, I thought of the thousands of Palestinians imprisoned by Israel, hundreds among them children, and many being held without reason."
Other Australians on board the flotilla allege they were denied food and water and physically assaulted.
Israel's National Security Minister Itamar Ben-Gvir, was also widely condemned after he posted a video of himself taunting detainees while they knelt with their heads on the ground, with their hands zip tied behind their backs.
Federal minister Mark Butler said the government had "in the strongest possible terms" raised its concerns both in Australia and Israel.
"The treatment of those Australians and people from many other countries as well has been disgraceful," he told ABC TV on Monday.
"We're really glad that the Australians are starting now to return home and reunite with their families, but this has been a particularly concerning event."
Israel's foreign ministry has labelled the flotilla a "provocation for the sake of provocation" and has previously denied the participants' allegations of abuse.
But members of the aid delegation are speaking with lawyers about their experience.
They want evidence collated to be used at the International Criminal Court to support the abuse claims of Palestinians.
While Mr McEwen did not yet know what the next steps would be for the flotilla mission, he said the push for Palestinian liberation was stronger than ever.
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