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.
"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.
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