During a major foreign policy speech to ambassadors gathered in Paris, Macron confirmed that French envoy Sylvain Itte was listening in from Niger capital Niamey despite being given a 48-hour deadline to leave the country last Friday.
"France and its diplomats have faced particularly difficult situations in some countries in recent months, from Sudan, where France has been exemplary, to Niger at this very moment, and I applaud your colleague and your colleagues who are listening from their posts," he said.
Niger President Mohamed Bazoum was toppled on July 26 and has been detained along with his family at the presidential palace in a coup that has been condemned by France and most of Niger's neighbors.
On Friday, Niger's foreign ministry announced that French ambassador Itte had 48 hours to leave, saying he had refused to meet with the new rulers and citing French government actions that were "contrary to the interests of Niger".
Macron insisted that France would not change position in condemning the coup and offering support to Bazoum, stressing he had been democratically elected and was being "courageous" by refusing to resign.
"Our policy is clear: we do not recognize the putschists," Macron said.