Members of Israel's Shayatet-13, or naval commanded, escorted the French yacht Dignite al Karama into the Ashdod Port Tuesday, Israel radio reports.
Navy senior official Brigadier-General Rani Ben Yehuda said that the boarding operation and takeover was restrained and that no weapons or humanitarian equipment were found on the ship.
"The takeover was performed after repeated warnings. After those were ignored the force approached the ship and boarded it while clearing the passengers. No one was hurt and no damage was caused to the vessel," Ben Yehuda said.
Ben Yehuda said it was the IDF's opinion that the flotilla was not over, but on the verge of dying down.
"There are still ships aiming to arrive. It’s an ongoing campaign. "
The Population, Immigration and Borders Authority said anti-Israel activists onboard the yacht are, effectively, entering Israel illegally. They face a hearing, deportation, and automatic blacklisting from Israel for a period of 10 years.
Officials added an Al Jazeera TV crew onboard the ship will not be deported from Israel.
In the past, Israel warned that all media personnel onboard flotilla vessels will be deported, but the decision was reversed without explanation.
Around 10:30 on Tuesday morning, IDF warships intercepted the French vessel, hailed it and informed it that is was nearing the Gaza blockade lines and must head to Ashdod Port or Egypt.
The IDF Spokesperson's Unit said that boarding operation took place some 65 kilometers off the Gaza coast and that naval commandoes followed procedure and took all necessary measures to ensure the safety of both soldiers and passengers.
The passengers were also offered food and drink after the commandos secured the vessel, the Spokesperson's Unit said.
The French Foreign Ministry said in response that Israel had informed it of the boarding operation. Eleven of the ship's 16 passengers are French citizens.
A statement of behalf of the ministry said France had advised its citizens not to take part in the flotilla due to personal security risks and noted that such flotillas can only increase tensions in the region.
France asked Israel to facilitate the quick return of its citizens.