During the offensive, rebels ransacked hospitals and health centers forcing medical staff to flee, Doctors Without Borders reported Tuesday.
The international organization said malnutrition and preventable diseases are rife in the country, with malaria being the leading cause of death.
"We are facing one of the worst years in terms of the impact of the disease," said Ellen van der Velden, the group's head of mission in the Central African Republic.
The majority of the country is without aid, the group said, because lack of security has forced U.N. agencies and many non-governmental agencies to withdraw to the capital.
The organization is calling on the international community to support the Central African Republic.