The US army said last week Dominic Ongwen had surrendered, marking a major success.
Thousands of people have died and more than a million fled their homes in central African country.
The victims include 15 local chiefs and three members of staff of Doctors Without Borders.
The UN proposes a nearly 12,000-strong peacekeeping force for the conflict-ravaged nation.
Mass killings have continued despite the presence of 2,000 French and 6,000 African Union peacekeepers.
Christian militia have carried out brutal reprisals against the Muslim minority.