BACKGROUND: Intractable pulmonary diseases with nontuberculous mycobacteria (NTM-PDs) and antimicrobial resistance have become increasingly concerning worldwide. Nevertheless, a surveillance system for NTM has not been established in most countries, thus requiring repeated, intermittent and time-consuming cross-sectional nationwide surveys. METHODS: To establish a nationwide surveillance system for NTM-associated diseases, we aimed to develop a prototype computer system primarily designed to continuously estimate NTM-PD incidence using a bacteriological case-defining algorithm through an automatic process of integrating bacteriological data collected from microbiology laboratories across Japan. To validate the accuracy of our study results, we compared the distribution of pulmonary tuberculosis cases between our laboratory data and the national surveillance data, which is representative of the Japanese population. RESULTS: Our estimates implied a 17.7% increase in NTM-PD incidence from 15.8 (14.9-16.8) in 2013 to 19.2 (18.2-20.4) in 2017, per 100 000 population. Moreover, 93.0% of the identified NTM-PD cases were dominated by the CONCLUSION: These findings, despite being laboratory-based, are extrapolatable to the general population in Japan and provide evidence that supports our system as a viable alternative to the nationwide NTM surveillance system.