Stoltenberg will be in Ankara on Monday to see Foreign Minister Mevlut Cavusoglu and in Athens on Tuesday for talks with Prime Minister Kyriakos Mitsotakis, his office said in a statement.
Greece and Turkey are both members of the Atlantic alliance but their own relations have plunged to new lows in recent weeks in a dispute over maritime borders and gas exploration.
Turkey's President Recep Tayyip Erdogan has revived a longstanding dispute about access to Greek waters around islands in the Aegean very close to Turkish shores.
Turkey deplored an exploration vessel with a naval escort to seek gas, infuriating Athens, and France deployed fighter jets to defend Greece and "EU sovereignty".
Tensions have begun to recede, after Germany led a European diplomatic outreach and Stoltenberg's NATO helped the neighbours set up a military hotline to head off accidental clashes.
But tensions are still high, and EU leaders meeting in Brussels on Thursday warned that Turkey could eventually face sanctions if its "provocations" persist.
Announcing the "de-confliction mechanism" on Thursday, Stoltenberg said it would "create the space for diplomatic efforts to address the underlying dispute and we stand ready to develop it further."
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