Abortion is not covered by the health insurance in Japan. Here is one of the proofs.
Although most of the services are covered by national insurance, some services, especially for non-diseases, cosmetic and luxury purposes, are not covered by health insurance and patients have to pay the full amount. A typical example is normal vaginal delivery, as childbirth is not considered as a disease....Other examples of direct payments include cosmetic surgery, orthodontics, abortions and infertility treatment.
Japan Health System Review, Asia Pacific Observatory on Health Systems and Policies, 2018