Macron also said western countries and NATO, which Turkey belongs to, have handled the crisis badly, with their Kurdish allies being abandoned.
"I consider that what has been going on for several days in the region is a serious mistake by the West and NATO," Macron said at the end of the summit.
"It weakens our credibility to find partners in the field who will fight with us, thinking that they are protected. It also questions how NATO works," he said.
Macron said Turkey's operation will be soon discussed in London with Turkey's President Recep Tayyip Erdogan during a meeting organized by France, Germany and Britain.
"It is important to get together and coordinate between the three Europeans and Turkey," he said. "We must try to see where Turkey wants to go, and how to bring it back to more reasonable positions.
"What the Turks are trying to do is madness."
EU Council President Donald Tusk said the "so-called" Syria ceasefire is "a demand (for) capitulation of the Kurds" and called on Turkey to immediately halt its operation in northern Syria.
After EU nations condemned Turkey's offensive in Syria, Tusk said a U.S.-Turkey agreement to lay down arms for five days was not a serious initiative.
"This so-called ceasefire, this is not what we expected," he said. "In fact it is not a cease-fire, it is a demand (for the) capitulation of the Kurds. We have to reiterate our call for Turkey to put a permanent end to its military action immediately and to withdraw its forces and respect international humanitarian law."
In its written conclusions, the Council said the unilateral Turkish action is undermining the fight against ISIS, therefore threatening European security.
Macron reaffirmed that foreign fighters from the Islamic State group who might flee Syrian detention centers and go to Iraq should be arrested and sent back to Syria for trial.
For those who attempt to reach France, "there's no direct airline from the Syrian camps to Paris-Charles de Gaulle (airport)", he said.
Macron said French members of the IS group who might go through Turkey on their way to France would be arrested and sent for trial in France, according to a cooperation agreement between France and Turkey.
After agreeing terms for a new Brexit deal on the U.K.'s departure from the bloc, EU leaders turned other thorny issues, including the bloc's budget and climate change.
No decision on the next long-term budget for 2021-2027 — a topic more divisive than Brexit — was adopted and the issue will be back on the agenda of the next planned summit in December.
Leaders need to find a compromise that satisfies countries in favor of minimal spending, those arguing that it must at least be maintained at the current level, and others fighting for increased contributions from members states to compensate for Britain's planned departure.
Sylvie Corbet in Paris contributed to this report.