Greek Prime Minister Alexis Tsipras and his Turkish counterpart Binali Yildirim agreed to strengthen ties in tourism, transport and energy at the talks.
The two countries are also working closely together on the TAP and Turkish Stream gas pipelines to carry gas into Europe through Turkey.
But the leaders did not hide their differences over a territorial dispute in the Aegean when speaking to journalists after their meeting.
While focusing on deepening commercial ties, the two countries need to work on resolving the Aegean dispute, said Tsipras.
He claimed that Turkish violations of Greek airspace and territorial waters in the Aegean Sea had increased over the last nine months.
"The Aegean must remain a sea of peace and stability," said Tsipras.
But territorial violations had occurred on both sides, according to Yildirim who said it was best to focus on areas of agreement.
He thanked Tsipras for his support in Turkey's bid to join the European Union while repeating his call for the EU to make good on its side of an agreement with Ankara to cut the flow of migrants from Turkish coasts into Europe.
Brussels had offered Turkey a three-billion euro package and a visa waiver for Turkish nationals if they helped migrants on Turkish soil so they did not move on into Europe.
Cyprus
The two leaders were cautious about upcoming talks on the thorny question of Cyprus, saying they hoped for a "fair and viable solution".
The United Nations is leading a new international meeting on the subject in Switzerland on June 28.
UN envoy Espen Barth Eide is pushing for a quick resolution of the question, calling the upcoming talks an "historic opportunity".
Guarantor powers Greece, Turkey and Britain will also attend the conference, as will a representative of the European Union as an observer.
The eastern Mediterranean island has been divided since 1974, when Turkish troops invaded its northern third in response to an Athens-inspired coup seeking union with Greece.
"We are seeking to open the way to providing solutions," Tsipras said of the upcoming Cyprus talks.
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