It said the boats would be towed to the Israeli port of Ashdod. The boats were “attempting to break the maritime security blockade that is in place in accordance with international law”.
The military said the takeover was peaceful.
Earlier in Gaza, an activist said protesters aboard the boats said they were surrounded by Israeli naval vessels. Then contact with the activists was lost when their satellite phones stopped working.
The Israeli military issued a short video clip showing a naval official calling on the ships to turn around.
“The Gaza area and coastal region are closed to maritime traffic as part of a blockade imposed for security purposes,” the unnamed officer said.
“Your attempt to enter the Gaza Strip by sea is a violation of international law. We remind you that humanitarian supplies can be delivered to the Gaza Strip by land, and you are welcome to enter (Israel’s) Ashdod port and deliver supplies through land crossings.”
Israel’s navy has intercepted similar protest ships in the past, towing them to an Israeli port and detaining participants.
Israel says its blockade of Gaza is necessary to prevent weapons from reaching militant groups like Hamas, the Iran-backed group that rules the territory.
Critics call the blockade collective punishment of Gaza’s residents.
Last year, nine Turkish pro-Palestinian activists were killed when they resisted an Israeli operation to halt a similar flotilla. Each side blamed the other for the violence.
The incident sparked an international outcry and forced Israel to ease its land blockade on Gaza.
Speaking after prayers at a Gaza City mosque, Ismail Haniyeh, the Hamas prime minister, addressed those aboard the boats, saying:
“Your message has been delivered whether you make it or not. The siege is unjust and must end.”