"We expect more meningitis cases to occur with the increasing summer heat," the ministry warned in a statement Saturday.
Unofficial reports said scores of people have already died of the disease in Juba, the capital city of the state of Bahr el Jebel in the south of the country.
The privately-owned Alwan newspaper reported Friday that 50 people had died in the town in two weeks. It put infections at 400 cases.
Fatalities were highest among children and elders, the paper said, adding that officials blamed the high death toll on shortage of drugs and venal solutions.
The officials have, however, declared the situation was brought under control by the arrival of drug shipments and doctors from the capital, Khartoum.
The outbreak was aggravated by a sharp rise in temperature in Juba that continued to record 42 degrees in the shade, the officials have said.
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