Israel said it would not allow “unauthorised boats” to enter the territorial waters of the Gaza Strip, the Jerusalem Post reported.
Swedish boat, named Marianne of Gothenburg, announced it set off from Sweden, to take part in the flotilla, several days ago.
Foreign Ministry spokesman Emmanuel Nachshon described the action as “unnecessary provocation”.
He added: “If the so-called helpful Gaza flotillas were really interested in the welfare of the population in Gaza, they would send their aid via Israel.”
According to the Israeli newspaper, the Israeli foreign ministry has appointed someone to coordinate policy on the matter between the foreign ministry, the prime minister’s office and the defence ministry.
In 2010, Israeli commandos attacked the Freedom Flotilla II when it entered Gaza’s territorial waters, killing ten people on board.
The Marianne is the first boat in the Freedom Flotilla III to leave for Gaza. It is scheduled to stop at ports in Helsingborg, Malmo and Copenhagen, as well as other ports that will be announced later. Other boats will join it on its journey.