We examined the relationship between a maternal alcohol-use diagnosis, and the timing of diagnosis, and child protection outcomes in a Western Australian population cohort. This analysis made use of routinely collected linked administrative health and child protection data. Those in scope for the study were women who had a birth recorded on the Western Australian Midwives Notification System (1983–2007). Women with an alcohol related diagnosis (ICD 9/10) on relevant datasets formed the exposed group. The comparison cohort were frequency matched to the exposed cohort. Generalized linear mixed models and a proportional hazards model were used to examine the relationship between a maternal alcohol-use diagnosis and subsequent child protection contact. Children of women with an alcohol-use diagnosis were at significantly increased risk of a substantiated child protection allegation (OR = 2.92, 95%CI = 2.71–3.14) and entry into out-of-home care (OR: 3.78, 95% CI = 3.46–4.13). The highest risk of child protection contact was associated with diagnoses received during pregnancy, and in the years immediately pre- or post-pregnancy. Children whose mothers have an alcohol-use diagnosis are at increased risk of contact with child protection services. Despite current public health recommendations, some women continue to drink heavily during pregnancy. Additional work is required to identify effective strategies to reduce heavy alcohol use in this population. Further, women who have been identified to have alcohol use issues require additional support, from multiple agencies, to reduce the potential negative impacts on their child.