Berlin added that all satellite phones on board had stopped working around 2 am, and said it was an external block placed on the lines.
The IDF had earlier announced it planned to disrupt the boats' communications as part of Israel's efforts to prevent the activists on board from speaking to the press. Berlin said they had other means of communication on board, but refused to elaborate.
She said all of the boats had set sail by 9:20 am, but that she did not know how long it would take to reach Gaza's shores. "The ships are pretty slow, they sail at a speed of around 20 nautical miles an hour," she said. On land, that is the equivalent of 37 kph.
The sailing already has been delayed several times. On Sunday morning live feed from one of the boats was renewed after having been off the air for a few hours.
Meanwhile the Navy is preparing to intercept the boats. One of the organizers, Dror Feiler, told Army Radio Sunday that the hundreds of pro-Palestinian activists aboard the ships will passively resist if Israeli seamen board the vessels.
"Israel has no right to invade the ships. It would be a foolish decision on its part," another activist said.
The organizers have claimed that unknown persons damaged two of the boats. One of them was forced to withdraw from the flotilla and the other docked at Cyprus's Turkish shore for repairs, causing further delay.
Many on board the flotilla accuse Israel of orchestrating most of the issues that have delayed the sail. But an Israeli official denied the claims, saying they were "a fiction created in order to make excuses for the flotilla's lacking organization".
AP contributed to this report