Fish mycobacteriosis should be considered as one possible means of transmission of mycobacterial infections to humans. In our study, we examined the survival of three field Mycobacterium avium subsp. hominissuis (MAH) isolates in fish meat during thermal processing technologies using culture and quantitative real-time PCR (qPCR) methods. Minced carp meat mixture was artificially contaminated with known amount of MAH cells and survival and absolute numbers of MAH was monitored after hot smoking and frying. The viability of MAH was significantly lower after the frying process, whereas in response to hot smoking viable MAH cells could still be cultured even after 10 min at 70 °C. Significant differences in thermal stability were also observed among the three different MAH isolates. The human isolate was the most resistant, whereas the environmental isolate was the least resistant, which is probably due to host adaptability. In this work we confirmed that MAH can survive temperatures of 70 °C and thus can pose a risk to consumers.