“I wish to avoid a rupture because (Turkey) is an essential partner in many crises we jointly face, specifically the migration challenge and the terrorist threat,” Macron told the Kathimerini newspaper.
The 39-year-old centrist acknowledged that Ankara had “objectively distanced itself” from the EU in recent months with “alarming deviations that cannot remain without consequence.”
He cited Turkey's desire to enter into a customs union with the EU as a possible area of retaliation.
In the wake of an attempted army coup against him last year, Turkish President Recep Tayyip Erdogan has pursued a crackdown on opponents in which thousands of people have been arrested or dismissed from their jobs.
A dozen German journalists and activists have also been arrested, fraying relations with Berlin.
German Chancellor Angela Merkel said over the weekend that she would ask the European Union to call off membership talks with Turkey, adding that “I don't see them ever joining”.
Macron said Thursday that he remained in “very regular contact” with Erdogan.
The EU and Turkey last year entered into an agreement which helped stem the flow of hundreds of thousands of refugees and migrants into Greece.
Ankara has threatened to rescind the deal at times when tensions have flared with Brussels over concerns of human rights abuses.
Macron was to hold talks later Thursday with Greek Prime Minister Alexis Tsipras and President Prokopis Pavlopoulos.
He is also scheduled to deliver a speech in the evening at the Pnyx, the hill opposite the Acropolis that served as Athens's parliament in antiquity.