The ships make up part of a second Global Sumud flotilla to try in recent months to break an Israeli blockade by carrying humanitarian aid to Palestinians in Gaza.
They sailed from the Spanish port of Barcelona on April 12.
The vessels were seized by Israel late on Wednesday in international waters off Greece's Peloponnese peninsula, which was hundreds of kilometres from Gaza, the flotilla's organisers said.
Israel's foreign ministry said it was taking about 175 activists from more than 20 boats taking part in the flotilla to Israel.
Six Australians were among those detained, from a total of 17 who were known to be volunteering on the flotilla.
"This is piracy," the group 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."
No state had the right to claim, police, or occupy international waters, but Israel had done that, extending its control outward to occupy the Mediterranean Sea off the coast of Europe, it said.
Israel's foreign ministry on Thursday called the flotilla organisers "professional provocateurs" and said its forces acted lawfully.
"Due to the large numbers of vessels participating in the flotilla and the risk of escalation, and the need to prevent the breach of a lawful blockade, an early action was required in accordance with international law."
Footage released by the organisers showed Israeli soldiers boarding a vessel and crew in life vests with their hands up.
Crew members were then taken to Israeli ships.
Greek government spokesman Pavlos Marinakis confirmed that 55 vessels were sailing some 90km off the Peloponnese towards Crete, shadowed by Israeli warships and Greek coastguard vessels late on Wednesday.
He said Athens had not been notified of the Israeli interception, which took place outside Greek jurisdiction.
A live tracker of the flotilla showed some boats sailing near the southwestern coast of Crete.
Turkey denounced the interception as a clear violation of international law which jeopardised navigational safety, adding it would take action to support the flotilla.
In October 2025, Israel's military halted a previous flotilla assembled by the same organisation, arresting Swedish activist Greta Thunberg and more than 450 participants.
That followed other seaborne attempts to reach blockaded Gaza.
Israel, which controls all access to the Gaza Strip, denies withholding supplies for its two million residents.
Yet Palestinians and international aid bodies say supplies reaching the territory are still insufficient, despite a ceasefire reached in October that included guarantees of increased aid.
with AP and AAP
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