We evaluated the prevalence and risk factors for child maltreatment in multiples aged 3 years and compared them to singletons in Japanese population-based data. Records on child maltreatment and health check-ups at 3 years of age from 17,125 singletons, 488 twins and 18 triplets were collected from a Public Health Center between April 2007 and March 2011. The associations of child maltreatment with potential risk factors were analyzed using the logistic regression model. Out of all children, 76 (4.31 per 1000) children had documented maltreatment including 69 (4.03 per 1000) singletons and seven (14.31 per 1000) twins. All of the cases in twins were physical abuse (100%) and nearly half of the cases (43%) included emotional abuse. Among twins, 86% of the biological mothers were suspected. The alleged perpetrators of twins showed a significantly higher rate of maternal depression compared to those of singletons. After adjusting the results for a number of potential biological and social risk factors, twins or triplets had a higher risk for maltreatment than singletons (OR 3.39, 95% CI [1.17, 9.83]). Healthcare providers should be aware that a multiple birth can place considerable stress on a family leading to child maltreatment and should provide appropriate support and intervention for mothers with multiples.