"We have formally declared the meningitis outbreak over," Isaac Adewole told reporters in the capital of Abuja on Wednesday.
Earlier in the week the Nigeria Centre for Disease Control said that emergency operations responding to the epidemic had been wound down following a decline in new cases.
"A total of 14,518 suspected cases of meningitis were reported from 25 states, with 1,166 deaths," said the centre in a statement.
Vaccination campaigns were carried out in Zamfara, Sokoto, Yobe and Katsina states, the worst affected by the outbreak.
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Meningitis is caused by different types of bacteria, six of which can cause epidemics. It is transmitted between people through coughs and sneezes, close contact and cramped living conditions.
The illness causes acute inflammation of the outer layers of the brain and spinal cord, with the most common symptoms being fever, headache and neck stiffness.
Nigeria lies in the so-called "meningitis belt" of sub- Saharan Africa, stretching from Senegal in the west to Ethiopia in the east, where outbreaks of the disease are a regular occurrence.
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