Vandals defaced a Beersheba memorial honoring Turkish troops who died in the Land of Israel during World War One. Police have launched an investigation.
"Kol Hakavod Letzahal (Well done IDF)" was spray-painted on the monument's base and the Turkish flag flown next to the Israeli one was burnt.
Beersheba Mayor Rubik Danilovich denounced the act as "violent and thuggish".
Former mayor Eliyahu Nawi said the act constitutes "a crime against the Jewish nation and Jewish history. Despite the current tensions with the Turkish government, we mustn't forget that after the expulsion from Spain only Turkey opened its gates to (the Jews).
"I call on the police to punish the vandals and urge the mayor to repair the damaged monument," he said.
About 1,000 people demonstrated Thursday evening outside Turkey's embassy in Tel Aviv, expressing their anger over Ankara's conduct in the wake of the raid on a Gaza-bound flotilla.
Some protestors hurled stones and a smoke grenade at the embassy. Three people were arrested by police at the scene, as mounted officers and riot police attempted to keep the demonstrators at bay.
Many of those present outside the Yarkon Street consulate held up Israeli flags and signs condemning the Turkish government. "Erdogan is a terrorist," some chanted, referring to Turkey's leader, while others chanted "Let the IDF win" and "Zoabi, go to Gaza," referring to the Arab-Israeli Knesset member who was aboard the raided ship.