Background In many middle-income countries, cancer incidence and mortality are rapidly increasing, but data for developing a strategy of cancer control are rarely collected or analyzed. This study aimed to identify factors associated with positive cancer screening for the uterine cervix and breast in Jakarta Province, Indonesia. Methods The data of 79,660 women who had visual inspection with acetic acid (VIA) and 83,043 women who had clinical breast examination (CBE) in the Jakarta Women Cancer Screening program in 2019 were included in this study. Socio-demographic factors, reproductive factors, lifestyle factors, family history, and the results of VIA and CBE were used for analyses. Binary and multivariate logistic regression analyses were performed to identify factors associated with VIA positive or CBE positive. Results The positive rate was 0.9% for both VIA and CBE among the screening participants. Factors associated with VIA positive were age < 30 years old, age at menarche ≤ 11 years old, remarriage, lower educational level, having an occupation, partner’s occupation other than being an employee, alcohol consumption, smoker, inadequate physical activity, cancer family history, and no Pap smear history. Factors associated with CBE positive were age at menarche ≤ 11 years old, widowed, high education, having an occupation, no breastfeeding history, birth control history, alcohol consumption, smoker, inadequate physical activity, cancer family history, and breast tumor history. Conclusion Factors associated with VIA positive and CBE positive among Indonesian women were revealed. To promote female cancer prevention in Indonesia, the prevalence of screenings should be increased and education about the risk factors should be provided to medical professionals.