BackgroundIntimate partner violence (IPV) against pregnant women is associated with many negative maternal and fetal outcomes and is a common public health problem all over the world. However, the issue has not been fully explored in Japan. This study aimed to explore the prevalence and risk factors of IPV against pregnant women in urban areas of Japan.MethodsThis study was a secondary data analysis of a cross-sectional survey that was conducted on women beyond 34 weeks’ gestation in five perinatal facilities in urban areas of Japan, from July to October 2015. The sample size was calculated to be 1230. The Violence Against Women Screen was used for IPV screening. Multiple logistic regression analysis was used to calculate the adjusted odds ratio (AOR) with 95% confidence interval (CI) for risks of IPV while adjusting for confounding factors.ResultsOf the 1346 women who participated in this study, 180 (13.4%) were identified as experiencing IPV. Compared to those who did not experience IPV (n= 1166 (86.6%)), women experiencing IPV had higher odds of being single mothers (AOR = 4.8; 95%CI: 2.0, 11.2), having lower household income (< 3 million yen, AOR = 2.6; 95%CI: 1.4, 4.6; ≥ 3 million yen and < 6 million yen, AOR = 1.9; 95%CI: 1.2, 2.9), having junior high school education background (AOR = 2.3; 95%CI: 1.0, 5.3) and being multipara (AOR = 1.6; 95%CI: 1.1, 2.4).Conclusions13.4%, or about one in seven women, experienced IPV while pregnant. This high proportion indicates the need for policy to address the issue of violence against pregnant women. There is an urgent need to build a system for the early detection of victims that offers appropriate support to prevent the recurrence of violence while encouraging victim recovery.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-16105-9.