Hawzah News Agency- Cameras broadcasting live feeds from the boats, verified by Reuters, showed armed Israeli soldiers in helmets and night vision goggles boarding the ships, while passengers huddled in life vests with their hands up.
Thunberg, 22, best known for her environmental protests, had pre-recorded a video that 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.
The Global Sumud Flotilla (GSF), 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.
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.
It was not clear how much aid it was carrying but it represented the highest-profile symbol of opposition to Israel's blockade of Gaza.
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 .
In a statement, Hamas expressed support for the activists and called Israel's interception of the flotilla a "criminal act", calling for public protests to condemn Israel.
The boats were about 70 nautical miles off Gaza when they were intercepted, inside a zone that Israel is policing to stop any boats approaching. The organisers said their communications, including the use of a live camera feed from some of the boats, had been scrambled.
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