Israel's ambassador to Ankara, Irit Lillian, has left Turkey along with other Israeli diplomats, Turkish broadcaster NTV and other media said on Thursday.
The Israeli embassy declined to comment on the reports.
Earlier this week, Israel's National Security Council issued a warning against travel to Turkey, citing fears that Israelis would be targeted by those angry at the conflict in Gaza.
It also urged Israeli citizens in Turkey to leave as soon as possible. Following the warning, Israeli airlines arranged flights from Istanbul late on Wednesday for Israelis who want to leave Turkey.
Turkish protesters have staged many anti-Israel demonstrations and Turkey has declared three days of mourning following a blast that killed large numbers of Palestinians at a Gaza hospital.