Anti-Balaka militias emerged after civil war broke out in 2013 with the declared aim of defending Christian communities from mostly Muslim rebels.
Before the violence erupted, Ngaissona briefly served as minister of sport under former president Francois Bozize, whose overthrow in 2013 by mainly Muslim Seleka rebels triggered the conflict.
The warrant issued in December is for "alleged criminal responsibility for war crimes and crimes against humanity which include murder, torture, mutilation, intentionally targeting and displacing civilians, pillaging and enlisting child soldiers.
The arrest comes just weeks after another suspected Central African militia leader Alfred Yekatom, known as Rambo -- was arrested and deported to The Hague.
In a statement, ICC Prosecutor Fatou Bensouda on Wednesday "welcomed" the arrest of Ngaissona.
"I am confident that pursuant to the domestic proceedings already underway in France, Mr Ngaïssona will be transferred to the ICC in due course to face justice," she said.