"A red line has been crossed, which is unacceptable," Macron said. "I urge all NATO partners to face up to the behaviour of a NATO member.
"France's response is to ask Turkey for an explanation on this point," he said.
Macron was speaking after a summit in Brussels at which EU leaders agreed to threaten Turkey with sanctions over its gas drilling in Cypriot waters.
But the French leader was also infuriated by events in disputed Nagorny Karabakh, where there has been heavy fighting between Armenian and Azerbaijani forces.
He alleged that intelligence reports had established that 300 Syrian fighters drawn from "jihadist groups" from the Syrian city of Aleppo had passed through the Turkish city of Gaziantep en route for Azerbaijan.
"These fighters are known, tracked and identified," he alleged, adding that he would call Turkey's President Recep Tayyip Erdogan "in the coming days."
Armenia has accused Turkey of sending mercenaries to back its ally Azerbaijan and on Monday the Britain-based Syrian Observatory for Human Rights said Ankara had dispatched at least 300 proxies from northern Syria.
Macron this week condemned what he called Turkey's "reckless and dangerous" statements backing Azerbaijan.
Nagorny Karabakh, a majority ethnic Armenian breakaway region inside Azerbaijan, declared independence after the fall of the Iron Curtain, sparking a war in the early 1990s that claimed 30,000 lives.
It is not recognised as independent by any country, including Armenia, and talks to resolve the conflict have largely stalled since a 1994 ceasefire agreement.
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