This study sought to determine the perception of the health providers in identified municipalities in Cebu Province, Philippines on the factors affecting vaccine hesitancy and acceptance. The immunization rate for the last three years under the Fully Immunized Child (Program) in the Fifth District of Cebu Province were analyzed and Focus Group Discussions with health care workers in the frontlines of the implementation of the program was done. As a healthcare provider, their confidence in delivering the vaccines is relevant to the sucess of any vaccination program, specifically with the current roll out of COVID-19 vaccines. Results revealed that there is a decline in the proportion of Fully Immunized Children starting 2018 to 2019 after the Dengvaxia fiasco. Since then, the fear in vaccines has created a domino effect in the decline in immunization accomplishments. Trends showed that health promotion activities and community engagement of relevant stakeholders can increase the immunization rates. In addition, the Focus Group Discussions resulted to 182 codes that are reported as three themes with two underlying subthemes. The factors that contribute to vaccine hesitancy and acceptance in the perception of health care providers is the track record of the efficacy and safety of the vaccines, people’s perceptions of credible information and their corresponding understanding of the nature and use of the vaccines. It is recommended that community vulnerabilities be assessed in the areas of the themes as reported as basis for the interventions to be introduced and utilize the themes identified in crafting and localization Risk communication stretegies for health workers and member of the community.