The outbreak started in the Ode-Irele town, Ondo state, and spread rapidly.
The disease – characterised by blurred vision, headache and loss of consciousness – killed the victims within 24 hours of falling ill.
Local health officials and World Health Organization experts are now in the town to try to identify the disease.
Laboratory tests have so far ruled out Ebola or any other virus, Ondo government spokesman Kayode Akinmade was quoted as saying by the AFP news agency.
He described the illness as “mysterious”.
WHO spokesman Gregory Hartl told AFP that all of those affected started showing symptoms between 13-15 April.