Cameras broadcasting live feeds from the boats, verified by Reuters, showed armed Israeli soldiers sporting helmets and night vision goggles boarding the ships, while passengers huddled together in life vests with their hands up.
A video from the Israeli foreign ministry showed Sweden's Thunberg, the most prominent of the flotilla's passengers, sitting on a deck surrounded by soldiers.
Thunberg, 22, best known for her environmental protests, had pre-recorded a video which was released on her behalf after her ship was boarded.
"If you are watching this video, I have been abducted and taken against my will by Israeli forces. Our humanitarian mission was non-violent and abiding by international law," she said.
Those vessels intercepted and those on board were expected to be taken initially to the Israeli port of Ashdod, where one ship was seen arriving by a Reuters witness.
"All the passengers are safe and in good health. They are making their way safely to Israel, from where they will be deported to Europe," the Israeli foreign ministry said on X.
"One last vessel of this provocation remains at a distance. If it approaches, its attempt to enter an active combat zone and breach the blockade will also be prevented," it added.
The Global Sumud Flotilla, the organiser of the voyage, said an estimated 443 volunteers had been detained, some of them transferred to one large cargo vessel before being taken ashore.
Turkish President Tayyip Erdogan on Thursday criticised Israeli aggression, saying it showed Israel's government has no intention of letting hopes for peace grow.
"I condemn the thuggery directed at the global Sumud Flotilla, which set out to draw attention to the barbarity of children dying of hunger in Gaza and to deliver humanitarian aid to the oppressed Palestinians," he said in a speech to officials from his AK Party in the capital Ankara.
The Istanbul chief prosecutor's office said it had launched an investigation into the detention of 24 Turkish citizens on the vessels, Turkey's state-owned Anadolu news agency reported.
South Africa's President Cyril Ramaphosa called on Israel to immediately release South Africans who were on the flotilla, including former president Nelson Mandela's grandson, Nkosi Zwelivelile Mandela.
The flotilla, which set sail in late August, is transporting medicine and food to Gaza and consists of more than 40 civilian vessels with parliamentarians, lawyers and activists.
Israeli officials have repeatedly denounced the mission as a stunt.Â
The flotilla's progress across the Mediterranean Sea garnered international attention as nations including Turkey, Spain and Italy sent boats or drones in case their nationals required assistance.
