The missions were in the Diocese of Bouar, about 270 miles from the capital, Bangui. They belong to the Capuchin Fathers and the Sisters of Charity of Saint Jeanne-Antide Thouret.
Many Muslims were forced out of the area at the height of violence in 2014.
On April 4, former fighters of Seleka, an alliance of rebel militias, invaded the small town of Ngaoundaye in the remote northwest part of the country. They set up camp at police headquarters and other places in the town, before occupying the missions and looting what they could, said Bishop Nestor-Desire Nongo-Aziagbia, vice president of the Central African Republic bishops' conference. He said the missions were attacked for economic reasons, not because they were Catholic.
"We keep repeating that the crisis has nothing to do with religion, but economic struggle for the exploitation of our natural resources. Control of the economic life of the country is what is at stake," the bishop said.
"The group of ex-Seleka was supported by members of Revolution and Justice, a militia group" of people from the country's northwest, Bishop Nongo-Aziagbia told Catholic News Service. "This is not the only action. There is a lot of insecurity for many people in CAR."
The ex-militia men had briefly kidnapped Congolese nuns as they entered the small town. Four people were allegedly killed before intervention by the U.N. Mission in Central Africa, whose job is to protect civilians.