Background: Outbreaks of vaccine preventable-disease control and elimination are impeded by impaired focal vaccination uptake. Therefore, we aimed at assessing vaccination uptake and comparing with passive surveillance (PS) report at village level. Methods: A community-based cross-sectional survey was conducted in the villages covered by two health centers in Bolikhamxay province, including non-Hmong and Hmong ethnic groups. Data collection was conducted by interviewing mothers or caregivers of children aged 6 to 23 months. The vaccination status was identified by vaccination cards, and compared with PS report at village level, which was collected from health centers. The Pearson’s chi-square test was used to compare these proportions, and pairwise correlation was used for the correlation of observed vaccination coverage. Finding: Sixteen villages were included, nine were from Luk52 health center area and 7 from Namkhou health center area. There was a significantly strong correlation for pentavalent pneumococcal conjugate vaccine, Japanese encephalitis, Measles and Rubella and full immunization coverage compared to others. This correlation was not observed in the non-Hmong population. Amongst non-Hmong, the recorded coverage was lower in PS than in the survey regardless of type of vaccine. In contrast, amongst Hmong most vaccines had higher recorded coverage in PS than in the survey except Bacillus Calmette–Guérin (BCG) and hepatitis B at birth dose. MR and JEV vaccine, commonly given at the same time, were the only one that did not have significantly different coverage between PS and the survey (p<0.334). Conclusion The mis-estimatation of immunization coverage from the PS reporting system highlights further research needed to determine a better indicator of village-level vaccination coverage, but measles could be an indicator of prioritizing the settings.