This paper presents seismic damage to continuous ceiling systems and the impact of damage on functionality in the hospital specimen tested at the E-Defense shaking table. The specimen had four ceiling systems with different peripheral constraint conditions, coverage areas, suspended lengths, and ceiling panel materials. The test results demonstrate that the continuous ceiling system is less susceptible to collapse than the lay-in ceiling system. However, medical facilities require maintaining functionality after earthquakes, and the consequence of damage as functional deterioration needs discussion. The twoelevation ceiling system across two rooms with different ceiling heights sustains severe damage at the rise-up part and the partition wall separating the rooms.The damage becomes severe when the ceilings at different heights vibrate at separate frequencies. The results highlight the enhancement of the lateral stiffness of the suspended ceiling at the rise-up part, such as by adding bracing bars. In the case of long-duration shakings assumed for far mega-earthquakes, damage accumulates with repeated loadings, and the functional loss by the damage becomes intense. This observation indicates that peak-related parameters (peak floor acceleration or peak floor velocity) do not comprehensively reflect the degree of damage in ceiling systems. The proposed functionality loss matrix highlights that the damage to the ceiling harms the aseptic environment for key medical rooms, especially for the cleanroom with extremely strict requirements on the air environment.