To establish biosafety risk-management guidelines for clinical departments of military central hospitals in China. Using failure mode and effects analysis (FMEA), we assessed the biosafety risk priority number (RPN) of clinical departments of three military central hospitals. Nosocomial infection (NI), medical substance-associated accident (MSA), medical technology misuse (MTM), and synthetic RPN were 0.50 to 4.37, 0.50 to 2.91, 0.50 to 3.42, and 0.64 to 3.28, respectively. NI prevention investment was negatively correlated with NI risk, while NI RPN was positively correlated with MSA RPN. There were significant differences between groups of departments in synthetic and MTM RPN. NI, MSA, and MTM constitute a hospital biosafety risk. However, their risk factors are distributed differently among departments. Traditional NI prevention investment can reduce NI risk, but such investments were not effective for MSA and MTM. Targeted measures need to be taken by referring to RPN and risk levels derived from FMEA.