The Philippines is frequented by natural disasters and around 74% of its population of more than 100 million is subject to various impacts from these disasters, and the country routinely ranks among the top 10 natural disaster-prone countries in the world. Mitigation efforts depend on a network of early-warning systems and on establishing mechanisms to respond more quickly to natural disasters. The latter concern, specifically disaster relief operations, is of utmost importance before, during and after a disaster and needs continual improvement of mechanisms for effective and efficient disaster response. In view of the need of government institutions involved to improve institutional mechanisms for immediate and effective disaster response, this study took on the interest to analyze the factors that significantly contribute to effective practices and innovative approaches in the implementation of the disaster response services. Structural Equation Modeling (SEM) approach was employed to examine these factors that influence the perceived effectiveness of disaster relief operations by integrating the Protection Motivation Theory (PMT) that is anchored on threat appraisal and coping appraisal, factors of which were incorporated in 29 survey questions fielded to 150 respondents who experienced disaster in flood-prone areas. Results showed that both appraisal and its factors had significant direct on stakeholder strategy which consequently has a mediating effect on the perceived effectiveness of disaster relief operations.