Mali's military leaders are expelling the French ambassador over what they called "outrageous" comments made by the French foreign minister about the transitional government, reports the BBC.
France said it was recalling Joel Meyer, who was given 72 hours to leave.
Foreign minister Jean-Yves Le Drian last week said the Mali junta was "illegitimate" and "out of control".
Western powers are also concerned about Russia's growing involvement in the former French colony.
Moscow reportedly sent military advisors in recent weeks to bolster local security forces in their fight with jihadist insurgents. Unconfirmed reports say hundreds of Russian mercenaries are also operating in the country.
France, which intervened in 2013 to support the government against the jihadists, plans to reduce its own troop deployment.
In another interview, Mr Le Drian accused Russian mercenaries of "helping themselves to the country's resources in exchange for protecting the junta".