The aim of this study was to conduct a nationwide survey in Japan of prefectural health centers, which were responsible for providing guidance to municipalities. The survey was performed in order to clarify the following issues: 1) the current level of support provided by prefectural centers for pre-and post-natal mental health; 2) the structures in place for providing consultation services for an “unwanted pregnancy” and the support available for high-risk cases; and 3) the advice available on postpartum maternal psychological screening, and interpretation of results of such screening. Questionnaires were sent by post to 394 prefectural health centers, of which 277 (70.3%) responded. A total of 32% of prefectural health centers confirmed that they had offered support to high-risk cases during pregnancy, and 72% had offered support post-partum. Regarding offering support to high-risk mothers, those prefectural health centers that did provide consultation services (n = 59) reported providing introductions and information about available facilities (P < 0.001) and conducting case conferences (P < 0.002). This was significantly different than prefectural health centers that did not provide consultation services (n = 198). At the prefectural health centers that “follow up on” the results of the mental health screening, psychiatry consultations were reported twice as often as the prefectural health centers that did “not follow up on” the results of mental health screening. These findings indicate that childcare support systems for postpartum mental health and the prevention of child abuse were established. However, the lack of prenatal health and support systems for the prenatal period remains an issue.