Macron insisted there must be no "ambiguity" toward IS, saying that Turkey's actions against the Kurdish militias that helped the allies fight the jihadist group showed the need for better coordination. The White House said they discussed "the importance of Turkey fulfilling its alliance commitments" as well as security and economic issues.
On Tuesday, Russian President Vladimir Putin said that NATO's expansion and beefing up of its military infrastructure near Russia's borders threatens the nation's security.
"Putin repeatedly pointed out that we are operating in a different way", he said.
What should have been a celebration of NATO's 70th birthday has been overshadowed by bitter rows about money and the future strategy of the alliance. "And sometimes they work with IS proxies", Macron said at a London news conference with US President Donald Trump.
Chief among them, Macron says, is "how to build sustainable peace in Europe".
Turkey has faced criticism among the allies at the London meeting and has threatened to impede a stronger defence policy for the Baltic states and the head-to-head was not on Trump's published agenda.
Macron and Turkish President Recep Tayyip Erdogan later came face to face at four-way talks with Germany's Chancellor Angela Merkel and Britain's Johnson.
The infighting is mostly due to Turkey's invasion of northern Syria.
The memorandum between Turkey and Libya on maritime boundaries in the eastern Mediterranean Sea will be sent to parliament "very soon", Turkey's deputy foreign minister said on Wednesday.
Professor Gulnur Aybet, foreign policy senior advisor to President Erdogan said however that the initial "leak" of the Baltic region defence plan had led to "misunderstandings" and made clear that the plan itself was part of an internal North Atlantic Treaty Organisation debate, though neither she or Stoltenberg spoke of how the issue could be solved.