The Integrated Medical Response protocol (IMP) is a new protocol of medical response during the response phase of a flood disaster in Kelantan, Malaysia. It integrates response workflows of various rescue agencies involved in patient care during response phase of flood disaster. Traditionally, health care services in this region used either an all-hazard protocol or those not specific to Kelantan. The present study is aimed to test the effectiveness of IMP on knowledge, attitude and practice of healthcare providers (HCP) involved in managing patients during flood disaster in Kelantan. This study was a prospective parallel group, single blinded, randomized controlled trial. The unit of randomization was the district within Kelantan on a 1:1 basis into either the control or intervention group using cluster randomized method. The hospitals within the district were subsequently assigned to the allocated group. Investigators were blinded to the assignments. The knowledge, attitude and practice scores of HCP were assessed by FloodDMQ-BM© and was evaluated 2 weeks before and immediately after a flood disaster table-top exercise. Data was analyzed using two-way repeated measure ANOVA. Our findings showed that intervention was essential to improve the knowledge [F (1,100) = 6.947, p-value 0.010 (<0.05)] and attitude scores [F (1,100) = 31.56, p-value 0.001]. Meanwhile, practice score was improved in both control and intervention group with time [F (1,100) = 226.56, p-value 0.001]. Thus, our localized IMP specific to response phase of flood disaster was crucial to further enhance the knowledge and attitude levels among HCP while practice level showed similar improvement in both control and intervention group post table-top exercise.