Objective: Incomplete primary immunization against vaccine preventable diseases is a significant public health problem. This study aimed to identify population at-risk for incomplete immunization and their associated factors. Methods: Data on immunization module from the National Health and Morbidity Survey (NHMS) 2016 was analysed. This survey was conducted as a nationwide community based survey using stratified random sampling design. Immunization history of children aged 12 to 23 months from the randomly selected addresses were taken from their mothers by face-to-face interview using mobile device. The information was verified with vaccination cards. Results: Out of 11,388 eligible respondents, 10,140 responded to the survey; 89.0% response rate. The prevalence of incomplete immunization was 4.5%, while non-immunised was 0.1%. Logistic regression analysis revealed that children at-risk of incomplete immunization or being non-immunised were girls, residing in urban areas, have mothers who do not believe that vaccine can prevent spread of disease and mothers who had pregnancy care at private healthcare facilities. Among reasons given for incomplete or non-uptake of immunization were due to either private healthcare facilities reasons; vaccine stock shortage or not due for immunization yet, or personal reasons; 'no time', forgotten', 'refused vaccine', and 'doubt halal status'. Conclusion: Children with incomplete immunization in Malaysia were more likely to come from urban areas and received care at private healthcare facilities. A standard schedule for all healthcare facilities and single registry may be suitable strategies to be implemented, in order to ensure high vaccination coverage in Malaysia.