Troops conducted house-to-house searches for several hours in a neighbourhood of Bangui believed to be a base for attacks against Muslims.
Automatic weapons, grenades, knives and ammunition were reportedly confiscated.
More than 250 military personnel were deployed in the disarmament drive.
The peacekeepers hope to secure the northern district of Boy Rabe.
It is a base for the anti-balaka militia - formed in response to killings by Muslim rebels and now blamed for their own revenge attacks.
However, operation was not entirely successful as some of the militia refused to disarm and one of its top leaders, Patrice Edouard Ngaissona, escaped capture.
The city's chief prosecutor said Mr Ngaissona was "the big fish who had to be detained", according to AFP news agency.
The United Nations refugee agency has described the situation as "a humanitarian catastrophe of unspeakable proportions".
The UN's World Food Programme says that about 1.3 million people - a quarter of the population - are in need of aid.
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