Background Although sense of coherence (SOC) moderates parental stress, the relationship between SOC, parental mental health and physical punishment of children with intellectual disabilities remains uncertain. The present authors describe parental physical punishment towards children with intellectual disabilities and investigate its related demographic characteristics, SOC and parental mental health. Materials and Methods With the cooperation of Tokyo's 10 special needs schools, the present authors obtained 648 questionnaire responses from parents of children with intellectual disabilities. Results Of the parents, 69.7% reported having physically punished their children with intellectual disabilities. This was positively associated with parents’ younger age, poorer mental health, lower SOC, children's younger age, birth order (firstborns) and disability type (autism/pervasive developmental disorder). Conclusions This is the first study supporting the relationship between SOC, mental health and physical punishment use among parents of children with intellectual disabilities. It may assist the development of strategies to prevent physical abuse of children with disabilities.