The facility in the city of Butembo was one of two centers torched by unknown assailants in the space of a few days, prompting Medecins Sans Frontieres (MSF) to suspend medical activities.
Aid workers have faced mistrust in some areas as they work to contain the Ebola outbreak, which has become the worst in Congo’s history.
The ministry said the Butembo treatment center reopened on Saturday. “For now it is managed by the ministry in collaboration with the World Health Organization and UNICEF,” it said in a statement.
MSF has not said when it might resume medical activities in the area.
The current Ebola epidemic, first declared last August, is believed to have killed at least 561 people so far and infected over 300 more.