Ambassador Joël Meyer has been asked to leave Mali within 72 hours, Mali's government said, citing French Foreign Minister Jean-Yves Le Drian's "hostile and outrageous statements".
The French foreign ministry said on Monday it had taken note of the decision and would recall its ambassador.
Le Drian told the broadcaster RTL on Friday that the status quo could not be maintained in view of the deteriorating political and military situation in Mali.
The former colonial power in much of the region, France has deployed its military to several parts of west Africa to assist in the fight against Islamist militias, with Mali a focal point.
The current French deployment in Mali, Operation Barkhane, involves 5100 soldiers, although officials in Paris intend to reduce that number to between 2500 and 3000 in the long run.
Mali's use of the Russian mercenary company Wagner has also been met with criticism in France, the UK, Germany and other countries.
The European Union imposed sanctions on Wagner in December, accusing it of fomenting violence and intimidating civilians in Mali.
Le Drian has said that France considered the deployment of mercenaries in Mali to be a security risk for the country and the region.
Jihadist groups regularly carry out attacks in Mali, Niger and Burkina Faso.
Mali has experienced three military coups since 2012.
The last one took place in May of last year.
