German Chancellor Angela Merkel has been left scrambling for ways to form a government after talks collapsed on Sunday, potentially forcing Europe's top economy into snap elections.
The difficulties complicate Macron's vision for EU reform which he set out in a speech in September that called for closer defence, political and economic ties as well as an institutional overhaul.
"We hope for Germany and for Europe that our main partner is stable and strong so we can move forward together," said a statement from the presidency.
Macron, who was elected in May, has been waiting for Merkel to form a government to start talks in earnest about his European plans.
The German leader had given tentative backing to his ideas of creating a new eurozone finance minister position and giving the 19-member zone its own budget, but the details are yet to be worked out.
France and Germany, the two biggest economies in the eurozone, are often referred to as the "motor" of the project and analysts say that little of consequence can be agreed before a German government is formed.
The German political situation "only reinforces the need for France to propose, to take the initiative and to work on an ambitious European project that we will put in place with our German partner," the statement from the French presidency added.
Speaking earlier in the day from his office in the Elysee palace, Macron told right-wing Republicans party Bernard Accoyer that "it is not in our interest that the situation becomes tense" in Germany.
Dominik Grillmayer, an expert at the Franco-German Institute in Ludwigsburg in Germany, said he was sceptical that Macron could advance without a German partner.
"Macron needs Merkel," he told AFP, adding: "I fear that the European Union is going to be paralysed for the next few months. Nothing is going to move forward on the reforms or the Brexit negotiations."