In this paper we measure, with a DEA BCC model, the economic efficiency of Embrapa’s (Brazilian Agricultural Research Corporation) research centers. We model the DEA economic efficiency as a linear function of the contextual variables revenue generation capacity, partnership intensity, improvement of administrative processes, cost rationalization, size and type of research centers. The model used is of the type dynamic panel and assumes a structured correlation matrix intra times and unstructured inter times. In order to better discriminate the efficient units we used a heuristic efficiency score that aggregates the efficiencies in relation to the original and inverted DEA frontiers. Partnerships positive effect in the efficiency scores does not confirm the thoughts that Embrapa’s performance evaluation process discourages the integration and cooperation of its research centers. From the point of view of statistical significance, the improvement of administrative processes is the most important indicator among the contextual variables.