This study describes shelter operations by public health nurses (PHNs) in Kesennuma City, located near the epicenter of the Great East Japan Earthquake, which occurred on March 11, 2011. The data were semi-structured interviews with 10 PHNs, 2 nutritionists, and 2 general administrators conducted from July 2013 to January 2014. All transcripts were analyzed using the constructivist grounded theory approach. We identified two operating methods for shelters: shelters stationed by PHNs in the Old City, and shelters patrolled by PHNs in the merged district. These methods were compared using four themes. In emergency situations, "operational periods," a predetermined short term for a leader to perform his/her duties responsibly, could be adopted for relatively small organizations on the frontline. PHNs must not only attempt to operate shelters on their own but also encourage residents to manage the shelters as well. Moreover, human resource allocation should be managed independently of personal factors, as strong relationships between shelter residents would sometimes disturb the flexibility of the response. Even when a situation requires PHNs to stay in shelters, frequent collecting of information and updating the plan according to response progress will help to maintain effective shelter operations.