At the Instituto de Pesquisa Clínica Evandro Chagas, a public research institute, a purposeful organizational change restructured productive activities into the form of Integrated Action Programs (briefly, PAIs). Taking into account the complexity of the new format, this article defines and computes managerial indicators to temporally assess those programs. Several optimization models were specified, considering efficiency frontiers with either constant or variable returns to scale. Findings suggest that PAIs are consistent with a pro-efficiency strategic path between 2002 and 2006. To that extent both the choice of PAIs as an organizational format and the adopted strategy may be considered successful.