The study examines the implementation of research programs of 15 partner institutions in Visayas and Mindanao in Regions 7,9,10,11,12,and 13. The study revealed that the partner institutions have established quality assurance mechanisms such as accreditation, ISO, and IQUAME. Their quality earned recognition by the Commission on Higher Education through grants of autonomy and deregulation. The implementation of the research programs of the 15 partner institutions is satisfactory, indicating that the mechanisms in place are not yet mature, robust, and sustainable despite management support, wellcrafted agenda, and adequate planning. The quality assurance mechanisms in place among the 15 partner institutions are not robust since it merely generated a satisfactory implementation of the research programs. This affirms the prognosis that research is still the weakest link even among the supposedly strong institutions. The strong management, agenda, and planning mechanisms are indicators that these schools have the potential to promote and achieve research excellence. The very satisfactory management and agenda are the distinguishing features that characterize autonomous and deregulated institutions in terms of research program implementation. The best practices in the implementation of the research programs include the following: management support, adequate fulltime personnel, release time for researchers, partnership and linkages, external consultants, locally relevant researches, niching of expertise, advocacy, attractive research compensation and rewards, annual review of the research agenda, research master plan, tracking system for researchers, quality assurance in the undergraduate level, research-based institutional innovations, and investment in faculty development.