Flotilla carrying pro-Palestinian activists, including a former Tunisian leader set to sail as early as Friday.
Israel has boarded and taken over a vessel attempting to break the blockade of the Gaza Strip, officials said.
In a statement the Israeli army said on Monday that it did not use force in redirecting the main boat Marianne to the Israeli city of Ashdod.
Petros Stergiou, a spokesperson for the flotilla, told Al Jazeera that organisers lost contact with the Marianne at around 2am local time on Monday morning, as three military boats approached.
— Freedom Flotilla (@GazaFFlotilla) June 29, 2015
“What we learned is that the Israeli navy attacked the Marianne around 100 nautical miles from the shore of Gaza,” Stergiou said.
“They said they could see three military boats approaching them that had identified themselves as being military.
“Once again, the Israeli government and its military has acted like state pirates and attacked our boat in international waters.”
Israeli army spokesman Peter Lerner said the seizure of the ship was “uneventful” and it would now be escorted to Ashdod in southern Israel.
After repeated appeals and following refusal to change course, the vessel is now being escorted to Ashdod Port.
— LTC (R) Peter Lerner (@LTCPeterLerner) June 29, 2015
Israeli Prime Minister Benjamin Netanyahu commended the Israeli navy for detaining the passengers on the ship.
“This flotilla is nothing but a demonstration of hypocrisy and lies that is only assisting the Hamas terrorist organisation and ignores all of the horrors in our region,” Netanyahu said.
The vessel is part of the Freedom Flotilla III – a convoy of four ships carrying pro-Palestinian activists including Arab Israeli lawmaker Basel Ghattas, Tunisia’s former president Moncef Marzouki and at least one European lawmaker.
In a similar bid to break the blockade in 2010, a pre-dawn raid by Israeli commandos on the Turkish ferry Mavi Marmara killed 10 Turkish activists.
In 2013, Israel apologised for “operational mistakes” in the raid. A compensation deal is still being negotiated between the two countries.
Israeli soldiers and officials who took part in the attack are being tried in absentia in Turkey for war crimes.
Several attempts since have been thwarted, but without bloodshed.
Mark Worley, in Doha, contributed to this story.