The Malaysian Government has initiated the National COVID-19 Immunisation Programme, known as PICK, to be a national strategy for addressing the spread of the coronavirus disease (COVID-19) pandemic across the country. Although the government intensified public awareness to increase program registration, the total number that registered in the state of Sabah, located in East Malaysia, was relatively low during August 2021, accounting for only 42.9% as compared to that of Peninsular Malaysia. Therefore, this paper examines the public perception toward the PICK program in Sabah based on 4 main components: safety, communication, psychology, and milieu. This study is based on the empirical findings drawn from 1024 respondents across Sabah using online Google Form surveys. This study adopts 5 methodologies for data analysis by using K-means clustering, mean score, Mann–Whitney U test, spatial analysis, and frequency analysis. It has been revealed that the percentage of respondents (categorized as Cluster 1) who have a negative perception toward the vaccination program is higher (55.9%) than those who have a positive perception (44.1%). This study further discovered that Cluster 1 has shown high skepticism regarding the vaccination program, which can be explained through the communication component (M = 3.33, SD = 0.588), especially Co2, Co3, Co1, and Co4. Following the communication factor, a chain of negative perceptions also affects other components such as safety, psychology, and milieu among Cluster 1, all of which contribute to poor participation in the PICK program. The study outcomes are extremely useful for informing local authorities to establish policies related to public interests, primarily in the areas of public health. Understanding the community’s perspectives and their obstacles in participating in such programs may assist local authorities in developing or implementing public policies and campaigns that ensure such related public programs can be conducted more effectively in the future.