Eleven ships were due to set sail this weekend, including nine from Greece, but two discovered damage to their propellers which activists blamed on Israeli sabotage.
Another ship was arrested on the high seas by the Greek coastguard for leaving port without permission, and the remainder were told they could not set sail.
Avigdor Lieberman, the Israeli foreign minister, claimed credit for the delays to the flotilla. "I welcome all the efforts that have been made to stop the flotilla," he said in a radio interview. "The success of these efforts on the diplomatic side are the fruits of intensive contacts with states in the region and the international community."
Israel is keen to prevent a repeat of the violent outcome to a similar attempt to break the blockade of Gaza last year, when its navy stormed the lead ship, killing nine Turkish activists.
Under what law the Greek government has instituted its ban on the ships leaving is unclear. "Ministers just decided that's what should happen," one international maritime lawyer said. "Everyone in the maritime law community here is pretty nonplussed."
Daniel Reisner, a lawyer at a leading Israeli firm said: "The decision taken by the Greek government is not founded in maritime law.
“If the Greek government has decided that letting these ships sail to Gaza would endanger the people on board, who the Greek government has a responsibility to protect, they are within their rights.
"But this is definitely new. I don’t know of any precedent.”
Dimitris Plionis, a spokesman for the flotilla, called the ban "preposterous". "Any ship can leave a Greek port legally without declaring their final destination," he said. "This is done daily by thousands of yachts and passenger and cruiser boats in Greece – they just given an immediate destination to the Port Authority and that's that."
A Greek foreign ministry statement said it acted out of concern for "the protection and safety of human life".
Activists criticised the arrest of John Klusmire, the captain of the Audacity of Hope, an American activists' boat, and the conditions under which he is being held in custody. The authorities said the boat had technical problems.
The coastguard said Mr Klusmire would be charged with trying to leave port without permission and endangering the lives of the boat's passengers.
Activists say they still intended to go ahead with the flotilla.
"The flotilla is still going on," said Mr Plionis, a spokesman. "We are sure there has been Israeli involvement in the Greek government's decision.
"The Israeli government has exerted pressure on the Greek government, as has the United States, and the Greek government has bowed. We consider that the siege of Gaza has been exported to the Greek shores."
Despite Mr Lieberman's comments, Mark Regev, the Israeli government spokesman, said the flotilla organisers were "missing the point" in claiming collusion.
"They have no international support except from the Hamas government in Gaza," he said. "What does that say? They lack any international credibility or legitimacy."