The Greek government had expressed hopes that the visit - the first to Greece by a Turkish president in 65 years - would help improve the often-frosty relations between the two neighbors. The NATO allies are divided by a series of decades-old issues, including territorial disputes in the Aegean Sea, and have come to the brink of war three times since the early 1970s.
But from the outset, the discussions focused on disagreements.
On the eve of his visit, Erdogan rattled his Greek hosts by telling Greece's Skai television that the 1923 Treaty of Lausanne should be "updated." The treaty delineated modern Turkey's borders and outlines the status of the Muslim minority in Greece and the Greek minority in Turkey, among other issues.
In a visibly testy first meeting with Greek President Prokopis Pavlopoulos, the two engaged in a thinly-veiled verbal spat over the treaty and Greece's Muslim minority, which Erdogan is to visit Friday.
"This happened in Lausanne, that happened in Lausanne. I get that, but let's now quickly do what is necessary," Erdogan told Pavlopoulos. "Many things have changed in 94 years. If we review these, I believe that all the sides will agree that so many things have to (change.)"
The spat continued during Erdogan's appearance at an unusually candid joint news conference with Prime Minister Alexis Tsipras.
The two listed a series of grievances their countries have with each other, including religious and minority rights, the divided island of Cyprus and the case of ten Turkish servicemen who have applied for asylum in Greece following a Turkish government crackdown after a failed coup last year.
"It is very important to strengthen our channels of communication, and this can only happen on the basis of mutual respect," Tsipras said.
The prime minister said the two also discussed tensions in the Aegean Sea, where Greece complains Turkish fighter jets frequently violate its airspace.
"The increasing violations of Greek airspace in the Aegean and particularly the simulated dogfights in the Aegean pose a threat to our relations, and particularly a threat to our pilots," Tsipras said.
For his part, Erdogan insisted once more that the Lausanne treaty needed to be reviewed, but stressed his country had no territorial claims on its smaller neighbor.
On the topic of the Muslim minority in Greece - which the country recognizes only as a religious minority, while Turkey has long pressed for better rights - Tsipras said his government agreed that improvements must be made in their quality of life.
"But issues that concern reforms involving Greek citizens are not an issue of negotiation between countries," he said.
Tsipras noted it was unclear exactly what Erdogan was seeking with his call to update the 1923 treaty.
"The truth is I am a little confused about what he is putting on the table," he said.
Greeks have been aghast at Erdogan's previous comments over possibly revising the Lausanne treaty, fearing that could harbor territorial claims.
Erdogan and Tsipras also sparred over Cyprus, a Mediterranean island divided since a 1974 Turkish invasion into a Turkish-occupied north and an internationally recognized Greek Cypriot south. Another round of internationally-brokered peace talks to reunify the island failed earlier this year.
"Who left the table? Southern Cyprus did ... we want the issue to reach a fair and lasting solution but that is not southern Cyprus' concern," Erdogan said.
Tsipras retorted: "My dear friend, Mr. President, we must not forget that this issue remains unresolved because 43 years ago there was an illegal invasion and occupation of the northern part of Cyprus."
Erdogan also raised the issue of Athens having no official mosque, to which Tsipras responded by saying Greece had restored several mosques around the country, including a centuries-old mosque in Athens.
The refugee crisis appeared to be the only issue the two sides did not disagree on, with both noting they had shared a significant burden of the migration flows into the European Union. More than a million people crossed from Turkey through Greece at the height of the crisis.
Later Thursday, several hundred leftist, anarchist and Kurdish protesters held a peaceful march through Athens against Erdogan's visit.
On Friday, Erdogan will visit the northeastern town of Komotini to meet with members of Greece's Muslim minority.
Suzan Fraser in Ankara, Turkey, Derek Gatopoulos and Nicholas Paphitis in Athens contributed.
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