Niger, which reopened airspace at the start of September, says it welcomes all commercial flights except for French planes or flights chartered by French companies.
Hours before France announced it was withdrawing its ambassadors and troops from Niger, the country's military rulers said that its airspace was closed to French aircraft.
Niger's airspace "is open to all national and international commercial flights except for French aircraft or aircraft chartered by France including those from the Air France fleet," the Agency for the Safety of Air Navigation in Africa and Madagascar (Asecna) said in a statement this weekend.
Niger also prohibits "any operational military flights and special flights" from any country without prior authorisation.
Relations between France and Niger deteriorated since the military overthrew President Mohamed Bazoum in a coup on 26 July.
France supported the Economic Community of West African States (Ecowas) that threatened military action to restore Bazoum, which lead Niger's military rulers to shut down the airpsace to all traffic on 4 August due "the threat of intervention from neighbouring countries".
Nearly a month later, Niger reopened its airspace to commercial flights, before announcing Sunday that French flights would not be permitted to fly over the country.
Air France, which suspended its flights to Niger on 7 August, told the AFP news agency that it was "not flying over Niger airspace".
As the main airline connecting Europe and Africa, Air France now cannot fly over half the airspace of the Sahel, with the closure of Libyan and Sudanese airspace, and security concerns about flying over Mali, forcing flights to fly over the Red Sea to the east, or the western coast of Africa and over Morocco and Algeria, increasing time delays and costs.
Meanwhile, the borders of Benin and Nigeria have remain closed since the Economic Community of West African States banned trade with Niger.
The cost of rice has since the week before the coup risen 21 percent, sorghum 24 percent, and maize 18 percent, according to the United Nations.
Despite these concerns, trade continues between landlocked Niger and other neighbours such as Algeria.