Turkish Ambassador to Tel Aviv Feridun Sinirlioglu and the consul general in Jerusalem arrived separately in Ankara "for regular and ordinary consultations", a Turkish official said.
They are due to return to their posts "in the course of the week", the official added.
Turkey has been Israel's chief regional ally for almost a decade.
Tensions have risen between the two countries after unprecedented harsh criticism by Turkish officials of crackdowns on the Palestinians in the Gaza Strip, which have claimed many civilian lives.
Last month, Turkish Prime Minister Recep Tayyip Erdogan described Israel's military operations as "state terror". Israel riposted saying the comment was "extremely regrettable".
Turkey then tried to temper the exchanges saying there was no change in its ties with Israel.
Bilateral relations reached their peak in 1996 when the two countries signed a military cooperation accord to the chagrin of many sections of the Muslim world.