Foreign Minister Yair Lapid said a "huge effort" by Israel's security forces had saved "Israeli lives in recent weeks", and thanked the Turkish government for its contribution.
He did not give further details. An Israeli security official told Reuters Turkey had arrested several suspected "operatives" of Iran's Revolutionary Guards.
"We are calling on Israelis not to fly to Istanbul - and if you don't have a vital reason, don't fly to Turkey. If you are already in Istanbul, return to Israel as soon as possible," Lapid said in a televised statement.
"These terrorist threats are aimed at vacationing Israelis. They are selecting, in a random but deliberate manner, Israeli citizens with a view to kidnapping or murdering them," he said.
"I want, from here, to relay a message to the Iranians as well. Whoever harms Israelis will not get away with it. Israel's long arm will get them, no matter where they are."
Tehran has vowed to retaliate against Israel, which it blames for the May 22 killing of Hassan Sayad Khodai, an Iranian Revolutionary Guards Corps colonel who was shot dead at the wheel of his car by two people on a motorcycle.
Israel neither confirmed nor denied responsibility, its standard policy over accusations of assassinations. It accused Khodai of having plotted attacks against its citizens worldwide.
Turkey is a popular tourist destination for Israelis. The two countries have been mending their ties after more than a decade of strained relations.Â
