Director-General for Preventive Health Services, John Rumunu, said the North African country and its partners were planning to conduct reactive measles vaccinations in the areas where the outbreaks have been reported.
He however did not confirm the number of cases or deaths in the areas.
Last week, Medical charity Médecins Sans Frontiers (MSF) said that 30 children with severe measles were being treated at its facility in Pibor area in eastern South Sudan.
The group said it treated the first children with suspected measles in central Pibor town in August, and the outbreak has grown significantly since then.
It called for an urgent vaccination campaign to stop the spread of the contagious disease.