Timely diagnosis of malaria is a strategy proposed by the World Health Organization to reduce malaria morbidity and mortality. A study was conducted to assess performance in microscopic diagnosis of malaria in the network of laboratories under the National Malaria Reference Laboratory of the National Institute of Health between 2012 and 2017. In the years of study, the laboratories obtained a rating of “acceptable” in the diagnosis of Plasmodium by 38.4%, 43.7%, 60.0%, 83.3%, 90.9%, and 95.8%, respectively, in the evaluation of species by 0%, 6.2%, 15.0%, 50.0%, 40.9%, and 54.1%, respectively; in stage assessment by 23.0%, 25.0%, 35.0%, 83.3%, 54.5%, and 79.1%, respectively; and in parasitic density assessment by 0%, 6.2%, 10.0%, 33.3%, 0%, and 12.5%, respectively. We conclude that in the period under evaluation, the percentage of laboratories that diagnosed and recognized the species and stage increases, which is not the case for recognition of parasitic density.