This quantitative survey described the occurring scenario among higher educational institutions having amalgamation as one of the strategies in rationalizing the Philippine higher education. The study dealt with the perceptions, issues, and perceived challenges of 90 administrators and 260 instructors/professors concerning amalgamation in Higher Education Institutions (HEIs) among the selected state universities and colleges in Region IV-A (CALABARZON) during the Academic Year 2017-2018. A researcher-constructed questionnaire served to gather the data. Weighted mean and ttest for independent means were employed to determine the differences on the perceptions of the respondents at 0.05 level of significance. Results indicated that the administrator-respondents were more aware of the idea of amalgamation than the instructor/professor-respondents. The respondents agreed in most of the items about amalgamation of HEI along access and equity, efficiency and effectiveness, relevance and responsiveness, utilization of resources, and quality and excellence. As to the issues on amalgamation, the administrators comparably perceived serious issues on amalgamation practices that needed urgent action such as delivery of projected student number, plans to meet financial and strategic goals, blueprint for the merged entity, governance and organization structure during the pre-merger phase, governance and organization structure during the transitional phase, quality assurance, and employees’ rights. A significant difference was found between the perception of the administrator- and instructor/professor-respondents towards the issues on amalgamation practices in terms of access and equity, efficiency and effectiveness, utilization of resources, quality and excellence, and blueprint of the merged entity.