BACKGROUND In June 2013, the fear of adverse events compelled the government to withdraw its recommendation of the Human papillomavirus (HPV) vaccine. Since then, the rate of vaccination among Japanese girls has dropped dramatically. OBJECTIVE This study aims to assess how the Japanese government's policy change against HPV vaccination influenced the degree to which parents in remote areas in Japan accepted the vaccine for their daughters, and to analyze related factors. METHODS A self-administered questionnaire was distributed to parents with daughters attending secondary schools or high schools in two remote areas of the country. RESULTS Out of 700 eligible parents, 246 (35%) responded. The percentage of parents in the "accept group" (those whose daughters had already been vaccinated or those who intended to have their daughters vaccinated) dropped from 54% before the government withdrew its HPV vaccine recommendation to only 4.5% after the withdrawal (1.5% of whom intended to vaccinate and 3% of whom had already had their daughters vaccinated). Vaccine acceptance was higher in parents who were employed as healthcare workers, had been educated through to the completion of high school, had good levels of knowledge about cervical cancer and the HPV vaccine, had low perceived barriers against the HPV vaccine, and received high levels of social support. CONCLUSIONS The acceptance of HPV vaccination among parents was low overall. Higher acceptance may be possible if the government restores its recommendation and healthcare providers disseminate appropriate information about the HPV vaccination and cervical cancer.