Israel's government cited a "high concrete threat" of a terror attack in Turkey and told citizens to leave immediately. Tourists have also been urged to postpone upcoming trips to the country.
The second warning in just over a week comes after three Israelis were among four people killed during a suicide bombing in Turkey's biggest city, Istanbul, on March 19.
In a statement issued Monday, Israel's Counter-terrorism Bureau said: "It has been decided to upgrade the existing travel warning vis-a-vis Turkey from a basic concrete threat to a high concrete threat."
The Bureau added that Turkish tourist sites were at risk from the self-declared "Islamic State" (IS) group, which it said had "high capabilities of carrying out further attacks."
The statement added that officials wanted to "reiterate our recommendation to the public to avoid visiting the country and - for Israelis currently in Turkey - to leave as soon as possible."
Despite strained diplomatic relations between the two countries, tens of thousands of Israelis visit Turkey each year.
The Istanbul blast on March 19 happened at a famous shopping street, and left dozens of others injured in addition to the four killed. The Turkish government said the bomber had links to IS.
Immediately after the bombing, Israeli Prime Minister Benjamin Netanyahu's office issued a generalized "level 3" warning against travel to Turkey.
But on Monday, this was raised to "level 2." If a "level 1" alert were by issued, that would urge citizens to leave the country immediately.
IS and Kurdish militants have been blamed for four bombings that have rocked Turkey over the past eight months, including a massacre at a peace rally in the capital Ankara in October that claimed 103 lives.
Meanwhile, a spokesman for Turkish President Recep Tayyip Erdogan said Monday that security forces had blocked other attacks in recent weeks, including planned suicide bombings.