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Ordinary people make moral judgments that are consistent with philosophical and legal principles. Do those judgments derive from the controlled application of principles, or do the principles derive from automatic judgments? As a case study, we explore the tendency to judge harmful actions morally worse than harmful omissions (the ‘omission effect’) using fMRI. Because ordinary people readily and spontaneously articulate this moral distinction it has been suggested that principled reasoning may drive subsequent judgments. If so, people who exhibit the largest omission effect should exhibit the greatest activation in regions associated with controlled cognition. Yet, we observed the opposite relationship: activation in the frontoparietal control network was associated with condemning harmful omissions—that is, with overriding the omission effect. These data suggest that the omission effect arises automatically, without the application of controlled cognition. However, controlled cognition is apparently used to overcome automatic judgment processes in order to condemn harmful omissions.