In a statement the Israeli army said on Monday that it did not use force in redirecting the main boat Marianne to 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.
"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."
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.