The Dignite al Karama, one of the ships which had intended to take part in a Gaza-bound international freedom flotilla, has left Greek island of Crete with about 10 pro-Palestinian activists on board.
Greek authorities banned all flotilla vessels from leaving the country's ports earlier this week, but the French ship was granted permission by the coast guard to sail to Rhodes on Saturday, Reuters reported.
But an activist on board said the boat's final destination was Gaza.
"We hope that we will reach that destination, but for the time being we are sailing within Greek waters," says Vangelis Pissias, a member of the flotilla's steering committee.
Eight ships remain blocked in Greek ports while a ninth sits in need of repair in a Turkish port after an apparent incident of sabotage.
Israel was also preparing to expel 120 mostly European activists detained after having managed to fly in Ben Gurion International Airport in Tel Aviv in a so-called "flytilla" protest.
On Saturday, police spokesman Micky Rosenfeld said 120 people had been denied entry and were waiting deportation with one or two days. Others had already been flown out, according to an immigration spokesperson.
Sabine Hadad, the immigration service spokesperson, said most of the activists were French, with the others being American, Belgian, Bulgarian, Dutch and Spanish.
Israel said it had been monitoring social media site and compiled a blacklist of persons they regarded as "provocateurs" intending to cause disturbances.
Organisers of the "flytilla," - officially called the "Welcome to Palestine" campaign - had said up to 800 activists were expected to fly into Ben Gurion airport in a peaceful mission to visit Palestinian families.
Israel provided airlines and foreign security agencies with a list of 342 "unwanted people," hoping they would be turned back at European airports.
At least 200 activists were halted in Europe by Friday evening, though a few dozen have reportedly managed to enter Israel so far, but further attempts are expected through Saturday.
Israeli authorities said they largely managed to pre-empt the campaign by foreign activists who are demonstrating for the right of access to the West Bank.
A statement from the Public Security Ministry quoted regional police chief Benzi Sau as saying a joint operation by police, the foreign ministry and transport officials "prevented the departure of hundreds of activists at their points of departure for Israel".
Meanwhile, hundreds of Palestinians and activists marched to the Qalandiya checkpoint in the West Bank a day after police stopped them from entering Israel.
Scuffles broke out after Israeli soldiers blocked the protesters close to the checkpoint and fired tear gas to disperse them. The activists say they want to draw attention to life under Israeli occupation.
Salah Khawaja, the "Welcome to Palestine" initiative organiser, said: "Today is the announcement of the beginning of a week-long movement against the apartheid system and racial discrimination.
"We have been preparing for this week months ago in the 'Welcome to Palestine' initiative to demonstrate to the world that Israel imposes an apartheid and racial system.
"And we have to continue our struggle and resistance to the wall, the occupation and their policies."
The protest marks the seventh anniversary of the International Court of Justice ruling that declared Israel's erection of the barrier on occupied land illegal.
Israel has re-routed the barrier several times in response to its own high court rulings on appeals from human rights groups that Palestinians are cut off from vital farmland or services.
The non-binding ruling found that building the barrier on land Israel occupied in the 1967 Middle East war was "contrary to international law", and urged Israel "to cease forthwith the works of construction of the wall" in the West Bank and Arab East Jerusalem.
The barrier has also drawn other international condemnation. Even Israel's main ally, the United States, has called it unhelpful.