"If something opposes the military chief of staff and the president, the military chief of staff goes," Macron, who as president is also the commander-in-chief of the armed forces, told Le Journal du Dimanche (JDD).
Macron said on Thursday that he would not tolerate public dissent from the military after General Pierre de Villiers reportedly told a parliament committee he would not let the government "fuck with" him on spending cuts.
De Villiers still has Macron's "full trust," the president told JDD, provided the top general "knows the chain of command and how it works."
"No one deserves to be blindly followed," De Villiers wrote in a message posted on his Facebook page on Friday.
De Villiers' last Facebook post is an open letter addressed to new military recruits that makes no mention of Macron. But it was perceived by French media as targeting the president's earlier comments.
De Villiers and Macron are scheduled to meet next Friday afternoon, according to the president's official agenda.
The French government trimmed the 2017 defense budget to ensure France meets its commitment to bring its budget deficit below the European Union cap of 3 percent of national income in 2017.
De Villiers, whose mandate as the military chief of staff was extended by a year on Wednesday by the new defense minister, criticized at a parliamentary committee hearing on the same day the 850-million-euro ($975 million) cut in this year's budget.