Israel still holds the other three non-Turkish vessels from the flotilla, as well as an Irish cargo ship, the Rachel Corrie, that sailed a few days later.
As the ships were released by Israel on Thursday, an Israeli official said the foreign ministry had sent Ankara "a message ... expressing Israel's expectation that Turkey will prevent other Turkish vessels from violating the naval blockade on the Gaza Strip.
"The message emphasises that Israel transfers equipment and goods to Gaza on an ongoing basis via the land crossings in a manner that is acceptable to the international community and which is anchored in recognised agreements," the official said.
The killings of the Turkish activists severely damaged Israel's ties with its only close Muslim ally.
The fallout from the raid has even affected Turkey's tourism, with the number of Israeli tourists visiting Turkey dropping by 90 per cent.
Only 2,605 Israeli citizens visited Turkey in June 2010, compared to 27,289 in June last year, the Turkish tourism ministry said.
In the first six months of the year, 75,071 Israelis came to Turkey, down 17.9 per cent from the 91,450 Israeli citizens who had travelled to Turkey during the same period last year.