Vaccine hesitancy seriously compromised the COVID-19 vaccine roll-out across the Western Pacific with limited evidence-based recommendations for diverse populations across the region. This study investigates the profile of the vaccine-hesitant populations by using fixed-effect latent class analysis and multi-country survey data collected in 12 countries in 2021 and 2022: Cambodia, Viet Nam, Lao PDR, Japan, Republic of Korea, Malaysia, Philippines, Mongolia, Fiji, Solomon Islands, Tonga and Vanuatu. The analysis identified 9 latent classes: Stay-at-home mothers, High-school-educated employees, High-school-educated older adults, High-school-educated young adults, University-educated employees, University-educated older adults, University-educated young adults, Unemployed, Non-compliant employees. The probabilities of COVID-19 vaccine acceptance and booster uptake were significantly lower in most of these latent classes, compared to University-educated older adults, as the reference group. While each country had unique compositions of latent classes among vaccine-hesitant people, there were also some shared risk groups, such as High-school-educated employees and High-school-educated young adults, across the countries. The study findings demonstrate the benefits of subgroup analysis in unpacking the complex interplay of characteristics within vaccine-hesitant populations, highlighting the need for customised strategies tailored to each country's unique profile of vaccine hesitancy.