"We have ended today in failure, it's a very bad image for both the Council and for Europe," Macron told reporters Monday after 18 hours of talks failed to break a stalemate over who should get the EU's top jobs.
However national interests, according to Macron, are getting in the way.
"It is clear that this failure is down sometimes to some personal ambitions," he added.
"When we are here, of course we all want to defend our country, but ultimately Europe's best interests should come first. This is impossible when there are so many hidden agendas."
Up for grabs also at the special summit in Brussels are the presidencies of the European Parliament, the European Council of EU governments, the EU's foreign policy chief and the head of the European Central Bank, which governs the euro currency.
Macron and Germany's Chancellor Angela Merkel came to Brussels after developing a plan on the sidelines of the G20 summit in Osaka, Japan.
Under the so-called "Sushi deal", the 28 EU leaders would nominate Dutch social democrat Frans Timmermans as president of the European Commission, rather than his conservative rival German MEP Manfred Weber.
But, when Merkel put this to fellow centre-right leaders in the EPP group immediately before the emergency summit, several rebelled, and the main summit was delayed as heads of government shuttled between side meetings.
The "preparation done at the Osaka summit was clearly not enough to iron out our differences," Macron said, admitting that he had been "hostile" to some candidates, implying Weber.
Some hope left
He stressed that the four candidates nominated by the leaders must include two women and someone from eastern Europe.
The outgoing group of EU officials was lopsidedly Italian, with Antonio Tajani holding the parliament top post, Mario Draghi head of the ECB and Federica Mogherini the EU foreign policy chief.
Top candidates include current prime ministers Stefan Lofven of Sweden and Andrej Plenkovic of Croatia. Others mentioned include Brexit negotiator Michel Barnier of France, Greens leader Ska Keller of Germany, Lithuanian President Dalia Grybauskaite and Margrethe Vestager, the EU’s competition chief since 2014.
The French President nonetheless remains confident that a deal will be reached when leaders reconvene on Tuesday, acknowledging that the next few hours will be "crucial."
A point of view shared by German Chancellor Angela Merkel who said that although the negotiations are "complex", she remains hopeful that with the "right amount of willpower, a compromise will be reached."
Monday's summit is the third attempt to fill Brussels' top jobs since the European elections in May.