BackgroundDespite the potential efficacy of hospital-based multidisciplinary child protection team (CPTs), research analyzing Japanese CPT databases is scarce. ObjectiveWe aimed to describe the characteristics of children and families reported to a CPT in Japan and investigate factors associated with the substantiation of maltreatment. Participants and settingThis retrospective, cross-sectional study took place in a national children's hospital in Japan and included 350 children who were reported to CPTs between April 2014 and March 2018. MethodsUnivariable and multivariable logistic regression analyses were conducted using the CPT database and medical records. ResultsAmong 350 cases, 33.4 % were substantiated. Children of <6 years of age comprised 73.4 % of the cases. The majority (67.7 %) received an injury-related diagnosis and physical maltreatment was suspected in 68.3 % of cases. In the univariable analysis, older age, a primary diagnosis other than injury, reporting department, psychological maltreatment, witnessing intimate partner violence, maltreatment by relatives other than biological father or mother, developmental disability, emotional/behavioral difficulty or psychological disorder, maternal/paternal psychological difficulty, and maternal history of maltreatment were significantly associated with substantiation. When adjusted for demographic, child and familial factors, a diagnosis other than injury (AOR 2.02, 95 % CI = 1. 11–3.65) and parental psychological difficulties (AOR 2.49, 95 % CI = 1.37–4.55) were independently associated with substantiation. ConclusionMost cases reported to our CPT were young children with an injury-related diagnosis. Substantiation was associated with a diagnosis other than injury and parental psychological difficulties. Further prospective and comprehensive studies are needed to establish universal guidelines for databases of hospital-based CPTs.