This study retrospectively analyzes the organizational handling of the COVID-19 pandemic by Mexico’s health authorities, from its outbreak in February 2020 to the final phase of the pandemic. The analysis begins with the undercounting of infected persons and deaths, which led to distorted figures and an abnormally high case fatality rate. The underestimation is examined separately for infections, deaths, and case fatality rates. The number of infected persons was affected by insufficient COVID-19 testing and restrictions on hospitalization. Death figures were evaluated by comparing mortality trends observed during the five years preceding the outbreak with the postpandemic data disaggregated by cause of death. These data were first collected by health authorities, reviewed by the Interinstitutional Group for the Estimation of Excess Mortality (GIEM, in Spanish), and later consolidated by the National Institute of Statistics and Geography (INEGI, in Spanish). The case fatality rate was calculated as the relationship between both variables on the basis of the original figures published by health authorities. After different calculation methods were explored, a more plausible estimate of the real COVID-19 death toll was established. Despite the need to correct the initial figures, the official database has not been updated. This lack of correction misinforms the public about the real impact of COVID-19 and risks leading the health system to repeat the statistical and organizational failures observed during the pandemic, potentially underestimating future health emergencies.