Cameras broadcasting live feeds from the boats, verified by Reuters, showed 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 the most prominent of the flotilla's passengers, Swedish climate campaigner Greta Thunberg, sitting on a deck surrounded by soldiers.
According to a tracker on the organiser, Global Sumud Flotilla's website, one boat was still sailing.
"Several vessels of the Hamas-Sumud flotilla have been safely stopped and their passengers are being transferred to an Israeli port," the Israeli foreign ministry said on X. "Greta and her friends are safe and healthy."
The Global Sumud Flotilla, transporting medicine and food to Gaza, consists of more than 40 civilian boats with about 500 parliamentarians, lawyers and activists.
The flotilla put out several videos on Telegram with messages from individuals aboard the various boats, some holding their passports stating that they have been abducted and taken to Israel against their will, and reiterating that their mission was a non-violent humanitarian cause.
Its 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, even as it triggered repeated warnings from Israel to turn back.
Turkey's foreign ministry called Israel's "attack" on the flotilla "an act of terror" that endangered the lives of innocent civilians.
The Istanbul chief prosecutor's office said it had launched an investigation into the detention of 24 Turkish citizens on board vessels in the flotilla on charges including deprivation of liberty, seizure of transport vehicles and damage to property, Turkey's state-owned Anadolu news agency reported.
Colombian President Gustavo Petro ordered the expulsion of Israel's entire diplomatic delegation following the detention of two Colombians in the flotilla. Israel has not had an ambassador in Colombia since last year.
Petro called the detentions a potential "new international crime" by Israeli Prime Minister Benjamin Netanyahu and demanded the release of the Colombians. He also terminated Colombia's free trade agreement with Israel.
Malaysian Prime Minister Anwar Ibrahim condemned Israel's interception of the flotilla, adding Israeli forces had detained eight Malaysians.
The flotilla is the latest sea-borne attempt to break Israel's blockade of Gaza, much of which has been turned into a wasteland by almost two years of war. Organisers denounced Wednesday's raid as a "war crime", saying the military used aggressive tactics, including the use of water cannon but that no one was harmed.
The flotilla also accused the Israeli navy of trying to sink the Maria Cristina boat. Reuters was not able to confirm the account independently.
The Israeli military did not immediately respond to a request for comment on the claim.
The boats were about 70 nautical miles off the war-ravaged enclave when they were intercepted, inside a zone that Israel is policing to stop any boats approaching. The organisers said their communications had been scrambled, including the use of a live camera feed from some of the boats.
The flotilla has repeatedly called on governments and international institutions demanding safety and release of unarmed humanitarians on the mission.
Last week the flotilla was attacked by drones, which dropped stun grenades and itching powder on the vessels, causing damage but no injuries.
Israel has imposed a naval blockade on Gaza since Hamas took control of the coastal enclave in 2007 and there have been several previous attempts by activists to deliver aid by sea.
In 2010, nine activists were killed after Israeli soldiers boarded a flotilla of six ships manned by 700 pro-Palestinian activists from 50 countries.
In June this year, Israeli naval forces detained Thunberg and 11 crew members from a small ship organised by a pro-Palestinian group called the Freedom Flotilla Coalition as they approached Gaza.
