On March 11, 2011, the Great East Japan Earthquake struck off the northeast coast of Japan. Within an hour of the earthquake, devastating tsunamis swept over the coastal region of the Miyagi Prefecture, facing Pacific Ocean. Accordingly, more than 400,000 residents were forced to stay at evacuation shelters. We investigated the changes in tuberculosis prevalence after the disaster. Annual data for all tuberculosis patients between April 1, 2009 and March 31, 2013 were extracted from the database of the Miyagi Prefectural Government. In the coastal region of Northern Miyagi, the number of tuberculosis patients increased in the post-disaster period (p < 0.001, 9.6 vs.19.1 per 100,000 people), compared to the pre-disaster period. In contrast, its prevalence did not change in the inland region of Northern Miyagi and the coastal and inland regions of Southern Miyagi. Importantly, in the inland and coastal regions of Northern Miyagi, the number of patients with latent tuberculosis infection (LTBI) increased in the post-disaster period (p < 0.001). Furthermore, in the coastal shelters, 11 evacuees with the history of contacting tuberculosis patients were diagnosed with LTBI, whereas no cases of LTBI patients were observed in the inland shelters. Thus, staying in the coastal shelters was a risk factor for contracting tuberculosis (OR: 19.31, 95% CI: 1.11-334.80); indeed, twice as many evacuees visited each coastal shelter on April 1, 2011, compared to the inland region. We should prepare the shelters to avoid overcrowding, and long-term observation is required to detect the prevalence of tuberculosis infection.