The joint research units between the Ontario Ministry of Agriculture, Food and Rural Areas and the University of Guelph increase efficiency and reduce duplication and operation costs. The joint research effort also enhances research excellence in order to meet the growing demands and the needs of the people and the Ontario agri-food industries, and to be competitive in the global market as these criteria are listed in the mandates of the two organizations. The Office of Research of the University sets priorities and administers the research proposal evaluation process of the partnership to set priorities for research proposals so that scarce resources are efficiently allocated across basic, applied, maintenance and service research. A weighted composite index scoring model, consisting of an analytic hierarchy process, congruence and scoring models, is presented in which criteria are transparent, and the process is analytically vigorous and clear so this process can be accepted by both the scientists and management. The criteria are articulated in the mandates and objectives of the two organizations. Efficiency of resource allocation is also estimated. Research projects are ranked according to their merit.