Eleven Australians were among 400 people detained by Israel last week in international waters west of Cyprus.
Video live-streamed to the Global Sumud Festival's website showed black-clad soldiers boarding the vessels while angles later taken by other flotilla participants revealed abandoned vessels bobbing in the sea as Palestinian flags flew in the wind.
Seven Australians are due to arrive in Sydney on Monday morning, while others will land in Melbourne and Brisbane.
Surya McEwen, a dual diagnosis care worker from Mullumbimby, is among those returning to Australia after his third attempt to deliver aid 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.
Other Australians on board the flotilla allege they were denied food and water and physically assaulted.
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.
"I am physically hurting a bit but also have a strong resolve.
"While I was imprisoned, I thought of the thousands of Palestinians imprisoned by Israel, hundreds among them children, and many being held without reason."
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.
"What we know about the human spirit is that when there is overwhelming horror happening for millions, like what has been happening in Gaza, it is part of the collective nature to find a way to intervene," he said.
"It's not that the dangers or the struggle of this movement makes it less likely for people to be involved. If anything, we have built more resolve to be stronger and more creative and thoughtful in the way we do this work.
"All that Israel has is violence but we have love, care, community and human solidarity ... (this movement) will definitely build and get stronger and the tactics will evolve."
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