Many of the victims are children, and the bacterial disease continues to spread - with more than 31,000 cases since January, but most of those being recorded in the last month.
The outbreak has affected at least 22 out of Nigeria’s 36 states, including the capital, Abuja.
According to the NCDC, the north of the country is being worst affected.
Nigeria's weak healthcare system has been struggling to cope - doctors in public hospitals are on strike and Covid-19 cases are increasing.
Devastating floods in some areas have also made things worse.