Crested penguins (Eudyptes spp.) have evolved a unique form of breeding in which the first of two eggs laid is much smaller than the second and has a higher likelihood of being lost during egg laying and incubation. In this study, we quantified aggressive behaviour in nesting Snares penguins and undertook an egg survival analysis to examine which factors influence egg loss. During 120 hours of observation of 50 nests, we recorded a total of 300 aggressive events in which females were repeatedly pecked, bitten and beaten. Aggressive events lasted from less than a minute to up to 55 minutes (mean 4.6 ± 7.4 min). Single males were the aggressor in 75% of aggressive events and in 50.7% of aggressive events the aggressor was identified as a neighbouring, breeding male. A greater percentage of the small first eggs (34%) were lost than the large second eggs (4%). We found that egg mortality was influenced by (i) whether the other egg within a nest had hatched, (ii) who was present at the nest (father, mother or both) and (iii) the average duration of aggressive events on the nest. When one egg within a nest had hatched, the other egg had a vastly increased mortality risk irrespective of aggression. However, long, aggressive events directed towards females after their partners had gone foraging, also increased the probability of egg loss. We suggest that the prolonged nest attendance by breeding males well beyond egg laying is in response to the high frequency of aggressive behaviour during this time. Our data show that A‐egg losses occur due to intraspecific aggression in this species. Further research is needed to clarify whether aggressive behaviour in breeding crested penguins is modulated by elevated testosterone levels in the males and whether any reproductive benefits accrue to the aggressors.