The International Criminal Court has acquitted a Congolese militia leader of all charges of leading fighters who destroyed a strategic village in eastern Congo in 2003, hacking to death and raping some 200 people including women and children.

Tuesday's acquittal of Mathieu Ngudjolo is only the second verdict in the court's 10-year history and the first time it has cleared a suspect.

Prosecutor Fatou Besnouda immediately indicated she would appeal and ask for Ngudjolo to be kept in custody.

Ngudjolo's acquittal comes as parts of eastern Congo remain virtual war zones even today, with rebel fighters believed to be backed by Rwanda locked in conflict with government forces.

Ngudjolo, wearing a suit and tie, stood up and showed no emotion as Presiding Judge Bruno Cotte acquitted him. (AP)