Background: Pseudo-outbreaks of non-tuberculous mycobacteria (NTM) in association with the water supply system in hospitals have been previously reported. We found that the frequency of NTM isolation in clinical samples increased after the reconstruction and renovation of a hospital in Japan in 2014. Aim: To analyse NTM, their possible relationship with the hospital water supply system, and outcomes of preventive measures. Methods: Environmental samples obtained from the water supply in hospital wards were tested for NTM. On obtaining positive results, the bacteria were further analysed using polymerase chain reaction (PCR). Findings: The PCR products of NTM showed that most samples tested positive for Mycobacterium paragordonae. Because none of the analysed patients developed any disease due to these bacteria, this event was considered a pseudo-outbreak. Investigation of the water supply system revealed that samples obtained from the recently attached aerators/ rectifiers during hospital renovation tested positive for these bacteria. Therefore, measures to remove aerators/rectifiers and prevent patients from drinking tap water in the hospital were introduced. Thereafter, the frequency of NTM-positive samples significantly decreased in the hospital. Conclusion:This study is one of the few reports which reveal the possibility of pseudooutbreaks of M. paragordonae in hospitals, hence raising the question whether aerators/rectifiers should be used in hospitals at all, because their mesh structure may promote NTM proliferation in supplied water. The importance of surveillance of bacteria derived from the environment, particularly after hospital reconstruction/renovation, is re-emphasized.