Israel's highest-ranking diplomat in Ankara was reprimanded on Monday by the Turkish Foreign Ministry, after seven Turkish nationals were refused entry to Ben Gurion Airport on Thursday.
Embassy charge d'affaires Amira Oron was also summoned to a meeting with the Foreign Ministry on Friday over the incident.
Israel confirmed the meeting took place, but refused to speak of its contents. Turkey, for its, part said it was a clarification meeting, which also included a rebuke of Israel's conduct.
The incident began when a group of nine Turks traveled to Israel to attend an event marking the Islamic holy month of Ramadan in Jerusalem. They were questioned for nine hours and, despite having the required visas, seven of them were sent back.
According to an Israel Security Agency (Shin Bet) official, those denied entry were suspected of having links to the Hamas terrorist group.
The incident at Ben Gurion Airport took place a day after Turkey confirmed it was holding talks with Israel over a deal to reconcile the two former allies.
While Turkey was clearly irked, diplomatic officials say the incident is not likely to affect efforts to promote relations between the two countries, which have been severely strained in recent years.