Background: Incomplete childhood immunization against communicable diseases is a major concern and vaccine hesitancy remains a hurdle to overcome in primary vaccination programs. This study was to examine the parents’ vaccine knowledge, awareness and hesitancy in relation to their children’s immunization status. Methods: A cross-sectional questionnaire study design was used. The parents who brought their children for immunization visit or follow-up at four public health clinics located in Sandakan district were invited to participate in this survey. Informed consent was obtained before each participant completed a hard copy of self-administered questionnaire in either English or Malay versions. Results: Of 405 parents responded, they generally had good knowledge and awareness of vaccines, only a small percentage (6.8%) of parents were found vaccine hesitant. There were significant differences in vaccine knowledge and awareness in those from different education levels and employment status; similarly, these two factors also significantly affected the vaccine hesitancy among the parents. The parents’ knowledge score was found to be moderately associated with their awareness (r = 0.551, p < 0.01) and inversely correlated to vaccine hesitancy (r = −0.397, p < 0.01). Most of the children (n = 376, 92.8%) in the study were immunized. The children’s immunization status was significantly associated with the parents’ education level (p = 0.025). There was also a significant difference in the total vaccine knowledge scores between the groups of parents with different child immunization status (p = 0.05). Conclusion: This study revealed that parents with higher education had a better knowledge of vaccinations, were less vaccine hesitant and were more likely to ensure that their children complete the recommended course of immunization. It is crucial to ensure parents are well-informed about the safety and efficacy of vaccines so that the children are protected from communicable diseases by the child vaccination program.