A dispute broke out last week between the two men just two months after Mr Macron was elected, just as France prepared for the military pomp of a Bastille Day parade where US President Donald Trump was the guest of honour.
After a clash between the new French President and head of France's armed forces over military budget cuts, the Military head Gen Philippe de Villiers has chose to resign from his post.
Without naming him directly, Macron upbraided de Villiers, saying to military officials: "It is not dignified to air certain debates in the public sphere".
Last week, de Villiers contested the cuts, part of 60 billion euros ($69 billion) in budget savings Macron hopes to make over five years, in a closed parliamentary hearing, the details of which were later leaked.More news: State police release drawing of suspect in Delphi killings
And in an interview published Sunday, Macron said: "If something comes in between the military chief of staff and the president, the military chief of staff [must] change".
But he had also said the general had his "full trust" as long as he "knows the chain of command and how it works". He is the first president since de Gaulle to neither serve in the armed forces nor do military service.
Mr. Macron has said that this year's proposed cuts are temporary and that he plans to increase spending in 2018. He promised a big increase in the defence budget over the next eight years.
The government said that Gen François Lecointre, who recently led French operations against Islamist militants in Mali, would take over as armed forces chief.More news: Street Fighter V adds Abigail from Final Fight on July 25
De Villiers, who has been in the position since 2014, added that he could no longer perform the functions of the job. "You can't publicly question a military leader like that in front of his subordinates". What are the defence cuts all about?
Macron, he said, had named Lecointre and also told ministers at a weekly cabinet meeting that he was still aiming to raise the defence budget to 2 percent of gross domestic product by 2025 despite cutbacks in 2017.
De Villiers issued statements criticizing the cuts and reportedly told a group of lawmakers in the French parliament: "I will not let myself be fucked like this!" according to Le Monde.More news: Iceberg bigger than Mayo breaks off Antarctic ice shelf