"We cannot remain militarily engaged alongside de facto authorities whose strategy and hidden objectives we do not share," Macron told reporters.
"The fight against terrorism can't justify everything."
The withdrawal will take between four to six months. France and allies will close down military bases in Gossi, Ménaka and Gao and transfer soldiers stationed there to Niger, according to Macron.
In a joint statement released earlier on Thursday, the European and Canadian governments involved in the Operation Barkhane and Takuba Task Force deemed that "the political, operational and legal conditions are no longer met to effectively continue their current military engagement in the fight against terrorism in Mali," resulting from obstructions by the Malian transitional authorities.
Notably, these countries pointed at the Malian transitional authorities' failure to fulfill their commitment to the international community and hold elections by February 27.
They nevertheless expressed their commitment to continue anti-terrorist operations in the Sahel region and their willingness to continue dialogue with the Malian transition authorities.
France first started anti-terrorist operations in Mali in 2013, under former President François Hollande.
But the relationship between Mali and French-led forces has deteriorated since the 2020 coup d'état and the subsequent establishment of a military junta in Mali, especially after the deployment of Russian mercenary group Wagner in Mali at the end of 2021.
French President Macron said he "completely rejects" the idea that France has failed in Mali after nearly nine years of intervention.
"(If France didn't intervene in 2013) you would for sure see the collapse of the Malian state," Macron said.
"At best we will have a territorial partition with a caliphate, at worst these terrorist groups will take full control of Mali."
Since French operations first began in 2013, 53 French soldiers have died in the Sahel region.