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This study aimed to clarify the population-based distributions of <i>Mycobacterium avium</i> and <i>Mycobacterium intracellulare</i> in Japan. We conducted a combined analysis of the national insurance claim and microbiological databases. The incidence rates of <i>M. avium</i> by province were similar throughout the country, with some exceptions, such as in Okinawa, probably because the bathing customs are different from those in mainland Japan. In contrast, <i>M. intracellulare</i> showed a gradual increase from the central part of the country to the southwestern region, with precise gradation, which may indicate infection sources in the natural environment. This study found that assessment of the infection route of <i>M. intracellulare</i> in the natural environment, which is similar to the distribution of <i>M. intracellular</i> patients, is warranted. In conclusion, improvement of the household environment could decrease the incidence of <i>M. avium</i>, while environmental countermeasures will be required to decrease the incidence of <i>M. intracellulare</i>.