Congolese government said on Tuesday Thomas Lubanga was arrested by security officials late on Saturday in the capital of the southwestern African country.
Lubanga, who heads the Union of Congolese Patriots, is being held at Kinshasa's notorious Makala prison, said government spokesman Henri Mova Sakanyi.
Lubanga is the latest of several militia chiefs arrested recently as Congo's struggling government and UN peacekeepers attempt to bring order to lawless Ituri province, where ethnic militias terrorise and prey on the local population.
Fighting between ethnic Lubanga's militia of Hema and Lendu militias in Ituri has killed more than 50,000 people since 1999 and made 600,000 homeless, aid groups say.
Fighters on both sides have been accused of killings, decapitation, torture, rape and forced labour.
Thousands are dying in Ituri every month, UN humanitarian chief Jan Egeland said last week, calling it the world's worst ongoing humanitarian crisis.