Turkey's Foreign Ministry summoned Israel's ambassador to complain about remarks by Defense Minister Ehud Barak suggesting the new head of Turkish intelligence could leak information to Iran, officials said on Tuesday.
Israeli envoy Gaby Levy was called to the ministry in Ankara on Monday.
"We expressed our discomfort and dissatisfaction with Barak's statement," a Turkish foreign ministry official, who declined to be named, told Reuters.
Barak made the comments at a closed-door briefing to party activists on July 25, reflecting the climate of mistrust between Israel and its once close ally.
The Israeli minister described Hakan Fidan, who was appointed head of Turkey's National Intelligence Organisation (MIT) in May, as a "friend of Iran."
In part of his speech broadcast by Israeli Army Radio, Barak expressed concern that secrets shared with Turkey "could become open to Iran over the next several months".
Already strained by Prime Minister Tayyip Erdogan's repeated criticism of the Jewish state's policies towards Palestinians, relations dived after Israeli naval commandos killed nine Turks aboard an aid ship trying to run a blockade of Gaza on May 31.
Fidan was previously a foreign policy adviser to Erdogan, and had served as Turkey's representative to the International Atomic Energy Agency.
He was also involved in talks that Turkey and Brazil held with Iran earlier this year to forge an agreement with the Islamic Republic for a nuclear fuel swap.