The west of Ivory Coast has also seen vicious battles between rival militias and ethnic groups. On Saturday, Caritas said its staff had found the bodies of hundreds of people in Duekoue, and estimated that 1,000 may have died.
The killings occurred between 27 March and 29 March in the Carrefour district, which was controlled at the time by fighters loyal to Mr Ouattara, spokesman Patrick Nicholson told the Associated Press.
"Caritas does not know who was responsible for the killing, but says a proper investigation must take place to establish the truth," he said.
Most of the 1,000 peacekeepers based in Duekoue had been protecting about 15,000 refugees at a Catholic mission there, Mr Nicholson added.
The International Committee of the Red Cross put the death toll at about 800, while the UN said more than 330 people were killed as Mr Ouattara's forces took over Duekoue, most of them at the hands of the rebels. However, more than 100 of them were killed by Mr Gbagbo's troops, it added.