Background Despite the increasing rate of exclusive breastfeeding practice in Indonesia, supportive interventions are still required. Breastfeeding self-efficacy of mothers is a key factor positively associated with optimum breastfeeding practices. Our analysis aims to assess the determinants of low breastfeeding self-efficacy amongst a sample of women with children aged under six months in Malang and Sidoarjo Districts, East Java, Indonesia. Methods We used information from 1210 mothers of children aged <6 months recruited in the BADUTA study conducted in 2015-2016 in Malang and Sidoarjo Districts. The outcome variable in this analysis was mothers' self-efficacy for breastfeeding using the 14 statements in the Breastfeeding Self Efficacy-Short Form. In total, 17 potential predictors of breastfeeding self-efficacy were evaluated, categorised into six sub-groups: (1) context/demographic variables; (2) household characteristics; (3) maternal characteristics; (4) child characteristics; (5) breastfeeding characteristics; and (6) antenatal and delivery care characteristics. Logistic regression analyses were employed to examine factors associated with mothers' self-efficacy with breastfeeding. Results More than half of the women had a low level of self-efficacy. Factors associated with low breastfeeding self-efficacy were low levels of education, i.e. completed primary school or lower (aOR=1.95, 95%CI: 1.20-3.15), completed junior high school aOR=2.30; 95%CI: 1.44-3.69), and completed senior high school (aOR=2.01, 95%CI: 1.34-3.00); working outside the house (aOR=1.72, 95% CI: 1.26-2.35); never received any advice on breastfeeding (aOR=1.37, 95%CI: 1.04-1.81) and low knowledge of breastfeeding (aOR=1.38, 95%CI: 1.04-1.85). Problems encountered with breastfeeding was also emerged as a significant predictor for low breastfeeding self-efficacy, either for mothers receiving solutions (aOR=2.16, 95%CI: 1.58-2.95) or those not receiving any solutions (aOR=2.65, 95% CI: 1.91-3.67). Furthermore, mothers who had cesarean section deliveries were more likely to have low breastfeeding self-efficacy (aOR=1.33, 95%CI: 1.06-1.68); while mothers exposed to three or more breastfeeding interventions were more likely to have a high level of breastfeeding self-efficacy (aOR=1.84, 95%CI: 1.03-3.27). Conclusions Multipronged breastfeeding education programs and support are required to improve women's self-efficacy with breastfeeding. Improved access to breastfeeding counsellors, active support for mothers following cesarean delivery, and increased supporting facilities at workplaces are essential to improve self-efficacy with breastfeeding.