Eleven Australians were among 400 people taking part in the Global Sumud Flotilla to Gaza before being intercepted by Israeli forces at gunpoint in international waters on Tuesday.
In a statement on Thursday night, the Australian Delegation for Global Sumud Flotilla said the Australians were being taken by bus to Ramon Airport in Israel, where they were expected to board flights bound for Istanbul, Turkey.
Earlier, Israel's ambassador to Australia Hillel Newman said the activists were "certainly safe", had access to consular officials and would be deported following due process.
"No one is in harm's way ... the dealing with them was very sensitive," he told reporters in Canberra on Thursday.
Israeli Prime Minister Benjamin Netanyahu and Foreign Minister Gideon Sa'ar condemned their colleague National Security Minister Itamar Ben-Gvir's humiliation of the activists as "not in line with Israel's values".
A social media post by Mr Ben-Gvir overnight showed him gloating over flotilla participants as they are forced to their knees by guards.
In the video, Mr Ben-Gvir, who remains a minister, walks through a crowd of detainees kneeling with their heads on the floor as he smiles and berates a man whose hands are zip-tied.
Jacinta McEwen - whose son Surya McEwen has taken part in the aid effort - said the parents of the detained activists were overcome with relief.
"But we are so angry that the reason our kids sailed in the first place is because of the failure of Foreign Minister Penny Wong and Prime Minister Anthony Albanese to show a spine as they watched children be murdered and starved to death," she said.
"We demand the government step up and do their jobs so the next lot of kids don't have to sail again in six months' time."
Mr McEwen has previously been detained by Israeli forces after taking part in other flotilla attempts.
Last time, he had his head slammed against a steel wall and a dislocated shoulder, a broken collarbone and broken ribs from being kicked in the chest, his mother said.
Palestinian-Australian Global Sumud Flotilla spokesperson Subhi Awad said Mr Ben-Gvir showed the world how Israel treated unarmed civilians aiming to deliver food.
"Imagine what they do to Palestinians every day off camera," the statement said.
Adalah Lawyers - a legal team acting for Arab minority rights in Israel - have received complaints from the flotilla activists about the use of tasers and rubber bullets, sexual harassment and degradation.
Foreign Minister Penny Wong has called for the release of the Australians after condemning the video posted by Mr Ben-Gvir.
"The images we have seen posted by Israeli Minister Ben-Gvir - who Australia has sanctioned - are shocking and unacceptable," Senator Wong said on X.
"We condemn his actions and the degrading actions of Israeli authorities towards those detained."
Senator Wong directed the Department of Foreign Affairs to call in Dr Newman to reinforce her message.
He met departmental officials in Canberra on Thursday.
The Executive Council of Australian Jewry slammed Mr Ben-Gvir for his "disgraceful" treatment of the activists.
"Nothing can excuse the appalling behaviour displayed by minister Ben-Gvir against a group of people who were being held in custody in Israel," president Daniel Aghion said.
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