The agency made the announcement via its Twitter handle at 12:01am on Thursday.
Fifty-three more persons were discharged, bringing the total from 481 to 534 recoveries, while the number of fatalities increased from 98 to 103.
More than 2,900 of the total number of cases were recorded between April 1 and May 6, a pointer to the increase in the number of samples tested.
According to the NCDC situation report for May 5, 2020, a total of 21,208 samples have been tested.
Lagos still accounts for a significant number of the country’s total figure with 1,308 confirmed cases, while Kano which confirmed its index case on April 11 now has 427 COVID-19 patients.
Lagos recorded the highest number of new cases on May 6 with 80 patients, while the Kano state ministry of health confirmed that the five deaths recorded on Wednesday occurred in the state.