Footage released Tuesday shows the harm done to the ship's propeller.
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Organizers of the flotilla claim Israel was responsible for the damage, which may leave the 25 activists prepared to board the ship, hailing from Greece, Sweden, and Norway, stranded in the port.
However Dror Feiler, a former Israeli and one of the flotilla's organizers, told Ynet that the ship "will take a few days to fix and then set off".
IDF chief: No poverty in Gaza
Defense Minister Ehud Barak called the flotilla a "provocation" Tuesday evening. He said the IDF was following events closely and that he had ordered it to stop the flotilla ships from docking in Gaza.
IDF Chief of Staff Benny Gantz said that "efforts at harming Israel's legitimacy are continuing, and the flotilla is an example".
"There is no poverty on the streets of Gaza – they have fancy cars and import televisions and LCD screens from Israel, and export agricultural products to Arab states. Whether our enemies' rifles be loaded with bullets or lies, the IDF will know how to deal with them," he said.
Earlier flotilla organizers reported that fewer than 300 activists will be participating in the sail, a much smaller number than originally expected. More cancellations are also likely to occur.
"The situation isn't good, it is true that we will sail with fewer passengers than the previous flotilla but aside from various reasons, we must remember that the Turks aren't participating so Israel won't be able to claim that this is an Islamist flotilla, so there are benefits," Dror Feiler told Ynet Tuesday afternoon.
Ahiya Raved contributed to this report
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