Recent experiences in disaster medicine in Japan have shown the importance of preventing post-disaster health deterioration among citizens during the evacuation and recovery phases. The effective involvement of various medical, social welfare, and nursing organizations is necessary to mitigate these health problems. This study explored the effectiveness of a time-tracking evaluation method for functional exercises in analyzing the communication and joint task-processing capabilities of various medical and social welfare organizations in response to a citywide heavy-rain disaster. Each exercise inject was analyzed in advance to create a task-processing chain according to the emergency medical response plan. The actions of the exercise players were then compared with the expected tasks in the processing chain. The exercise created overload for some player groups. The completion rates and average execution times of the tasks were compared across task types and player groups, indicating the potential weaknesses of the current emergency operation plan. Responses of local medical associations to similar exercise injects were compared to analyze the range of diversity in responses and the merits of past exercise participation. Although the results of this time-tracking evaluation need to be carefully interpreted by combining the results regarding the quality of players' exercise actions, this method provides a new perspective for evaluating emergency operation plans through functional exercises.