Japan has repeatedly suffered from natural disasters. A number of temporary evacuation shelters have been opened for the benefit of evacuees. Although the operation of such evacuation shelters has improved after the Great Hanshin-Awaji Earthquake (1995), a number of operational difficulties were encountered during the Great East Japan Earthquake in 2011 and the Kumamoto Earthquake in 2016. A systematic literature review was conducted to identify the medical concerns encountered in temporary evacuation shelters by focusing on unsanitary environment, food and nutrition, and shortage of medication. Actual sanitary conditions have been found to be below the standards stipulated by the Japanese government as per international guidelines. Food aid in evacuation shelters was neither nutritionally balanced, nor was the distribution to different shelters balanced. Furthermore, evacuees with chronic diseases feared that there may be a shortage of medication. Crowding in evacuation shelters increased the risk of outbreaks of infectious diseases (e.g., tuberculosis). Malnutrition and shortage of medication exacerbated the risk of deterioration of chronic diseases (e.g., diabetes mellitus, hypertension) among evacuees. Therefore, it is recommended that healthcare professionals should be promptly deployed to evacuation shelters, to promote sanitary control and education, as well as address limited space availability, and food and medication shortage.