"I put to the Turkish president this increase in Turkish violations in the Aegean .. And we finally agreed to give emphasis to our efforts to reduce tensions," Tsipras told a news conference in Brussels.
The two countries, which are members of the military alliance, are at odds over a host of issues ranging from ethnically split Cyprus to sovereignty over airspace and overflights.
Turkey says its jets carry out regular patrols along the Aegean as part of its right to protect its borders.
While tensions have long simmered, the rhetoric between the two neighbours has sharpened in the past two years: Two Greek soldiers detained by Turkey and eight Turkish soldiers seeking asylum in Greece have been the focal point of verbal jousting in recent months.
The meeting with Erdogan, which lasted almost two hours, was not "the easiest of meetings", Tsipras told journalists.
The Greek soldiers were arrested in March after crossing a borderline between the two countries and face charges of illegal entry in Turkey.
The eight Turkish commandos, who commandeered a helicopter to flee Turkey as a coup against Erdogan crumbled in July 2016, have sought asylum in Greece. Turkey says they were involved in the putsch and demands they be returned to face trial.
Tsipras said he raised the issue of the Greek soldiers, whom, he said, were in custody without charge. In turn, he said, Erdogan raised the matter of the Turkish commandos who fled to Greece.
"I stressed, once more, I made clear, that in Greece, the Greek judiciary is totally independent," Tsipras said, referring to applications by those individuals to claim asylum.
"At the same time I underlined what I have repeatedly stated, that for the Greek government, coupists, from any country - from Turkey in this case - or anyone who attempts the breakdown of democratic order, are not welcome in our country."
The two countries also agreed that their foreign ministers maintain contact on ethnically-split Cyprus, divided since a Turkish invasion in 1974 after a brief Greek-inspired coup. The latest bid to unite the island under a federal umbrella collapsed exactly one year ago.