Foreign ministry spokesman Yigal Palmor said that Israel's Ambassador to Ankara Gabby Levy had spelled out their worries in a meeting with Turkish officials earlier this week.
"The ambassador told his Turkish counterparts about our concerns about the dispatching of a pro-Hamas flotilla in the coming months," he told AFP.
Organisers say the so-called "Freedom Flotilla II" will include participants from 50 countries who will try to reach Gaza next month, exactly a year after a previous attempt ended in disaster when Israeli troops stormed the lead ship and shot dead nine Turkish activists.
The new flotilla is believed to include some 15 ships, compared with six last year.
The initiative was an "incitement to violence", said Palmor, echoing remarks made on Monday by Israeli Prime Minister Benjamin Netanyahu.
The naval convoy was "not a peace flotilla but a provocation, a deliberate provocation to seek to ignite this part of the Middle East", Netanyahu told a delegation of EU heads of mission in Jerusalem.
"I think it's something that you should ... transmit to your governments, that this flotilla must be stopped."
Netanyahu has also called on UN chief Ban Ki-moon to help stop the flotilla.
Israel imposed a blockade on Gaza in June 2006 and restrictions on imports and exports were tightened a year later when Hamas seized power in the territory of 1.5 million people, ousting loyalists of Palestinian president Mahmud Abbas.
In the face of international condemnation of its raid on the flotilla, Israel eased some of its restrictions on goods entering and leaving Gaza.
But it maintains tight restrictions on items it says could be used by Hamas, including some building materials, and continues to control Gaza's airspace and sea access.