The International Criminal Court, which issued the warrant, did not give details of Patrice-Edouard Ngaissona's arrest or what he was doing in France. Ngaissona is expected to be transferred to the court's detention center in The Hague once French authorities complete the needed formalities.
The court said in a statement that Ngaissona was the most senior leader and "National General Coordinator" of the anti-Balaka militia when crimes such as murder and torture took place in the Central African Republic's west for about a year starting around December 2013.
The group is accused of targeting Muslims in interreligious and intercommunal fighting that broke out in 2013, when predominantly Muslim Seleka rebels seized power in the Central African Republic's capital, Bangui. The violence left thousands dead and displaced hundreds of thousands more.
Ngaissona is head of his country's national soccer federation. In February, he was elected to the executive committee of the Confederation of African Football, the governing body for soccer on the continent.
"Many in the Central African Republic claimed Nagaissona was 'untouchable,' given his senior post at the Confederation of African Football, but even high level figures implicated in grave crimes can be arrested to face justice," said Lewis Mudge, senior researcher in the Africa Division of Human Rights Watch. "Now, we look to the ICC prosecutor's office to continue its crucial work, particularly to pursue perpetrators of crimes from all parties to the conflict."
The court said a panel of judges that reviewed evidence and approved the arrest warrant "found reasonable grounds to believe that Mr. Ngaissona is liable" for involvement in crimes that include murder, enforced disappearances, using child soldiers and attacking humanitarian aid workers.
The court's prosecutor, Fatou Bensouda, said the arrest "further attests to our resolve to respond - concretely - to the calls of countless victims seeking justice for such crimes in CAR." Amnesty International, which named Ngaissona and 19 others as possible war crimes suspects in 2014, called the arrest a "major step forward in the fight against impunity in the Central African Republic." Another anti-Balaka leader, Alfred Yekatom, was sent to the International Criminal Court last month.
The human rights group said "ongoing serious violence in CAR - including an attack on a displaced persons camp that killed up to 100 civilians in Alindao last month - is a testament to what happens when impunity reigns."
The former French colony's government asked the ICC in May 2014 to investigate crimes allegedly committed by both the Seleka and the anti-Balaka. So far, no Seleka fighters have been publicly targeted by the court's chief prosecutor, Fatou Bensouda.