Over the past two decades, considerable investigation has been undertaken into the research training of higher degree research students in many parts of the world. However, in developing nations the exploration has been far more limited, particularly concerning the kinds of issues and challenges their higher education systems face. This makes the Philippines an important case, where it is a national priority to develop university research and improve research training practices. This study examined research training in the Philippines from a policy perspective. The study sheds light on the nature of research training of developing nations by (1) describing the context in which it is situated, (2) identifying and examining the issues, challenges that confront government and universities, (3) evaluating the implications of these issues and challenges, and (4) providing recommendations to improve university research and research training in the country. The study’s findings confirm that public and private higher education institutions in the Philippines are largely engaged in teaching while research is a less intense university activity. The current context of university research and research training indicates that the structure of graduate education and training needs improvement in policy and practice domains. The government and universities need to develop new policies and improve practices regarding both staff research training and professional development, and student research education and training. A range of issues and challenges confronting the government and universities have been identified by this study concerning funding, infrastructure, academic staff development, research supervision, student support, quality assurance in research, collaboration and partnerships, research ethics, intellectual property, and research priorities. The most important challenges for government and universities relate to effectively meeting the dual demands of teaching and research, building a critical mass of researchers, and developing excellent research skills and competences among staff and students. The findings from this study have also informed the creation of a timeline that depicts key points in the candidature of masters and doctorate students, particularly identifying coursework, research, and supervision phases, and has identified contributors to the development of student and staff research skills. Together, these provide a basis for considering current and potential research training initiatives. Overall, the study provides a new and comprehensive analysis of the policy issues in research and research training and offering suggestions for advancing policy and practice.