The row erupted at the weekend after Turkish Prime Minister Prime Recep Tayyip Erdogan again criticised the military "coup" in Egypt that ousted president Mohamed Morsi in July.
Egypt kicked out the Turkish ambassador, prompting Ankara to declare the Egyptian envoy "persona non grata" and downgrading diplomatic relations.
The Turkish envoy Huseyin Avni Botsali landed in Istanbul late yesterday and left the airport without making any comments, the foreign ministry said.
Turkish President Abdullah Gul has voiced hope that relations would be put on a better footing soon, saying after Egypt's decision on Saturday that the situation was "temporary".
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"We will not stop saying what is right and standing by the Egyptian people just because the coup-installed government in Egypt is disturbed," he said on Tuesday.
Erdogan's Islamic-rooted government had forged an alliance with Morsi and his Muslim Brotherhood after the Islamist leader won Egypt's first free presidential election in June last year.
Turkey, a predominantly Sunni Muslim country, has found itself increasingly isolated in the Middle East and now has no ambassadors in Egypt, Israel and Syria.