The rapid rise of chronic diseases in the Philippines from non-communicable disease to mental health disorder requires a rebalancing of health care priorities to meet these challenges. Recent statistical modelling studies in the country revealed a strong relationship in the developmental outcome of NCD and mental health. The need to develop strategies aimed at integrating NCD and mental health are important steps towards efficient and effective health care delivery systems particularly in low-income countries. Critical to these changes in health care delivery system is the role of key decision makers in understanding the interrelationship of chronic diseases and areas in public health policy related to governance. A semi-structured key informant interview was conducted, and responses were analyzed using a thematic content technique to determine knowledge and how current health programs are meeting these challenges. The results of the study highlighted areas for future research and public health policy development, while revealing structural and organizational problems. The implication of improving human capital development, governance, and communication gaps between national and local government agencies are vital to addressing these problems.