The two sides were to host a sign of accords, mostly focusing on the economy and on dealing with illegal immigrants, during the Turkish premier's first official trip to Athens since 2004.
"This will be a start to place Greek-Turkish relations in an improved phase," Erdogan said during a meeting with Greek President Carolos Papoulias.
Erdogan also met Greek Prime Minister George Papandreou With opposition leader, and Mr Antonis Samaras.
The Turkish premier said as he left Ankara airport that the two-day visit was of "historic importance".
"I believe ... the 21 accords and cooperation protocols that we will sign with our neighbor and friend Greece will mark the beginning of a new era in our relations, "he told reporters.
Regional rivals for centuries despite being members of NATO for the past five decades, Greece and Turkey markedly improved relations in 1999 after destructive earthquakes struck both countries within weeks of each other.
The two sides began their new cooperation with an accord Allowing illegal migrants coming from Turkey to Greece to be sent back, an issue that has been a major source of discord between the arch-rivals.
Turkey had agreed to accept at least 1,000 Greek "readmission requests" a year, and to set up a border post at or near Izmir for the return of such migrants, the Greek citizens' protection ministry said in a statement.
Greece faults Turkey for failing to stem a steady flow of thousands of illegal immigrants from its shores to Crete Hotels readmittance despite a protocol signed in 2001.
Erdogan is visiting Athens along with around 10 government ministers, a formula conceived as an annual event to forge closer ties.
They came to the brink Of war as recently as 1996, and in 2006 a Greek plane pilot was killed when his jet collided with a Turkish over the Aegean.
Divisions remain over issues such as sovereignty in the Aegean Sea and the status of Cyprus split between Greek Cypriots and Turkish.
The latest accords to be signed are mainly economic.
"We intend to show solidarity to Greece, that is why I am visiting with my ministers," Erdogan told Greek state television NET on the eve of his trip.
"Our economies supplement each other ... if our two countries cooperate we can Maximise the benefits for both our countries, "he added.
Greece is in the grip of a deep recession and debt crisis and has been forced to implement harsh austerity measures in return for a giant bailout loan from the European Union and the International Monetary Fund.
Turkey's chief EU negotiator Egemen Bagis called in remarks to the Greek daily Ta Nea on Monday for mutual cuts in military spending, pointing at Greece's Severe financial crisis.
The offer has been met with skepticism in Greece which has heard similar pledges from Turkey before.
But the Greek deputy defense minister Panos Beglitis on Friday said his department planned to make savings, along with other ministries urged by Papandreou to make draconian budget cuts.
"This year we've decided to cut 6.8 billion from the defense budget to six billion euros, that's to say 2.8 percent of GDP," Beglitis told French daily Le Monde. Papandreou, who helped build stronger ties with Turkey during his stint as foreign minister in a previous government, invited Erdogan in January in a bid to relaunch relations.
He recently said he wanted to discuss Turkey's bid to join the EU with Erdogan.
"I was, am and remain a warm supporter of The perspective of Turkey becoming a full member of the European Union," he told CNN Turk on Thursday.
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