A statement by the Israeli military said there was not any violence during the incident, in which Israeli troops had boarded, and then searched the boat while forcing it to sail to one of their ports.
Activists said the vessel had Europeans that included politicians and was on the way to Gaza, the Palestinian territory that has been blockaded.
The statement released early Monday by Israel said that after exhausting every diplomatic channel the government ordered its Navy to redirect the flotilla to prevent a breach of its naval blockade in Gaza.
Israel said the troops that boarded the vessel escorted it to Ashdod a southern port. The flotilla of four vessels was the latest in a number of protest voyages in the Mediterranean against the nine-year blockade of Gaza, which is dominated by Islamist Hamas.
One of the incidents became deadly five years ago when 10 activists from Turkey were killed on one ship that the Israeli Navy had commandeered in the Mediterranean.
A statement released earlier by the International Solidarity Movement a pro-Palestinian organization said the flotilla was led by a fishing trawler with 50 activists from 17 different countries including a lawmaker who is Israeli-Arab.
The boats, said the activists, set sail on June 27 with solar panels on board to help alleviate some of the serious problems of electricity across the Gaza strip. The cargo also included medical equipment for the territory, which is home to over 1.7 million Palestinians.
Benjamin Netanyahu the Prime Minister of Israel issued a prepared statement that congratulated his troops for taking control of the ship he said had been involved in what he called a demonstration of hypocrisy and the support for Hamas. He said that the actions by Israel followed the accords of international law.