Abstract: Objective The study provides a representative and objective summary of the omission rates of infectious disease reports to facilitate the assessment of the performance of public health at all governmental levels. Methods The randomized survey was performed in diverse medical institutions based on the Fujian Omitted Reports of Infectious Diseases in Medical Institutions Survey Program by selected investigating officers from the Fujian Provincial Center for Disease Control and Prevention. Results A total of 366 omitted cases were found among 3114 inspected cases of infectious diseases in Fujian, the overall omission rate of infectious disease report being 11.8%, with an increase of compared with the rate last year (5.2%). The lowest omission rate was recorded in provincial medical institutions, 2.5%, followed by the county (district) level institutions, 10.6%, while the highest rate was in township institutions, 16.6%. The average outpatient registration rate of medical institutions was 74.5%. Conclusion The omission rate of infectious disease report in medical institutions is higher than that of last year, which is a reflection of the current condition of infectious disease reports in various medical institutions. The outpatient registration rate is relatively low, requiring an established system to ensure better implementation of outpatient registration.