In Japan, influenza vaccination is offered to children and pregnant women at clinics or hospitals as an elective, self-funded treatment, as the vaccination is not included in the national vaccination subsidy program. However, some Japanese municipalities offer a discretionary subsidy for seasonal influenza vaccination of children and pregnant women as a local policy. We identified these local subsidy programs during 2019/2020 seasonal influenza season by conducting a cross-sectional survey across Japan. Out of a total of 1741 municipalities, responses were received from 1732; therefore, the response rate was 99.5%. The local influenza vaccine subsidy programs for children were offered in 45.7%, and for pregnant women in 10.2%, of Japanese municipalities. This is the first survey of subsidy programs for pregnant women. While policy diffusion of subsidy programs for children was observed during the 9 years since a previous study, such programs for pregnant women remain limited. Despite many municipalities having subsidy programs, we found that their provision still remains limited when viewed as a whole.