This paper compares the proposed by the Colombian Institute for Science at Technology development named Colciencias methodology to measure the efficiency in the scientific research groups with the Data Envelopment Analysis approach. As a study case, both approaches are applied to the officially accepted by Colciencias research groups of the Pereira Technological University, in the period 2000 through 2003. The ranking of the groups is obtained by both approaches and the results are compared and analyzed.