Macron previously attempted to bridge the European Union's differences with Moscow this summer, warning against the "strategic error" of isolating Russian Federation and describing Russian Federation as "deeply European".
Failing to open communication channels with Moscow would be a "huge mistake", Macron said, despite suspicions from Poland and other former Soviet-bloc states in the EU.
"Things that were unthinkable five years ago - to be wearing ourselves out over Brexit, to have Europe finding it so hard to move forward, to have an American ally turning its back on us so quickly on strategic issues - nobody would have believed this possible".
Macron's questioning of Nato's effectiveness and suggestion that European countries in the 29-member alliance should reassess their situation come ahead of a key summit with leaders including Donald Trump in Britain early next month. With most of NATO's member countries failing to chip in their promised 2 percent of GDP, Germany announced on Thursday it hopes to hit that target for the first time by 2031 - seven years later than the date agreed upon by the alliance's members in 2014.
It spends more on its defence budget than all the others combined.
But after talks with Stoltenberg in Berlin, Merkel said, "The French president chose drastic words". His decision to pull the USA out of the Paris climate agreement particularly annoyed Macron.
And Macron said he believed that Putin, for all the anti-Western bombast from the Kremlin, would find his strategic options limited, in the long term, to "a partnership project with Europe".
Stoltenberg attempted to smooth over the "differences of opinion and divisions among North Atlantic Treaty Organisation allies", suggesting Macron's declaration the alliance is on its deathbed is just another issue - like climate change, or the war in Syria - on which countries might have conflicting approaches.
Stoltenberg meanwhile stressed that "NATO is strong", adding that the United States and Europe were working "more together than we have done for decades". If we don't wake up ... there's a considerable risk that in the long run we will disappear geopolitically, or at least that we will no longer be in control of our destiny.
"I welcome European unity, I welcome efforts to strengthen European defense, but European unity can not replace trans-Atlantic unity", he added.