Introduction: Many children with disabilities and latent characteristics are cared for in nursery schools (daycare centres). Paediatricians commissioned by nursery schools in our previous survey proved the occurrence of disabled children abused in schools. As the parents of the alleged victims were likely to contact the municipality, a survey of the municipalities managing childcare was requested.
 Methods: The target group was local authorities' childcare service management departments (public authorities). Questionnaires were sent twice to 1,742 municipalities from late 2012 to the fiscal year (FY) 2014. Incidents were collected by inquiring about implementing preventive measures and reasonable accommodations.
 Results: The number of municipalities that responded was 490 and 595, respectively, and 38 and 7 municipalities received complaints from parents that instructors had abused their children with disabilities. Based on the number of reports, the incidence of abuse in nursery schools in 2014 was estimated to be 0.0077% (95% CI: 0.0059–0.0094) and 0.0208% (0.0073–0.0344) for children with disabilities. In the 2014-2015 research periods, more teachers and staff were made aware of the consultation service as a preventive measure, and more emphasis was placed on the informed consent of parents as a reasonable accommodation. Regional characteristics, classified by the percentage of children, influenced the implementation of some measures.
 Conclusion: The incidence in Japan was estimated to be lower than in other countries.