Israel has launched air strikes and ground incursions to keep Syrian forces away from its border. Turkey is a key backer of the Islamist-led coalition in Syria that toppled Bashar al-Assad in December.
Turkish Foreign Minister Hakan Fidan confirmed the talks in comments to CNN-Turk television late Wednesday.
While Turkey was carrying out "certain operations in Syria", there had to be a way of heading off conflict with Israel "which is flying its planes in that region -- just as we do with the Americans and the Russians", he said.
A Turkish defence ministry source said Thursday that the first technical meeting with Israel had taken place in Azerbaijan on Wednesday.
A statement from Israeli Prime Minister Benjamin Netanyahu's office also confirmed the talks.
They had "agreed to continue on the path of dialogue in order to maintain regional stability", said the statement.
But Fidan, in his comments, said this did not mean the two sides were moving toward normalising ties strained over Israel's war against Hamas in Gaza.
Turkey has suspended all trade with Israel, President Recep Tayyip Erdogan accusing Netanyahu of "state terror" and "genocide" in Gaza since the October 7, 2023 Hamas attacks on Israel.
On Monday, US President Donald Trump offered himself as a mediator between Israel and Turkey.
Speaking alongside key ally Netanyahu at the White House, Trump touted his "great relations" with Erdogan as an avenue for negotiations.
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