Background: Community health workers (CHWs), hailing from the general populace, play a pivotal role in fortifying healthcare systems, with a primary focus on mitigating non-communicable diseases (NCDs) and elevating overall life expectancy. To assess the aptitude of CHWs in NCD prevention, we introduced the Community Health Workers Perceptual and Behavioral Competency Scale for preventing non-communicable diseases (COCS-N). This study examines the multifaceted interplay of individual and community factors that influence CHWs’ COCS-N scores. Methods: The research design is a secondary analysis using data from a self-administered questionnaire survey of 6480 CHWs residing in municipalities across Japan, which obtained 3120 valid responses, between September to November 2020. The COCS-N was employed as the dependent variable, while the independent variables were individual-related factors, including years of community health work, health literacy, and community-related factors, such as CHWs’ sense of community. To ascertain the significance of associations between individual and community factors and CHWs’ competency, an analysis of covariance (ANCOVA) was utilized to compare the three groups Q1/Q2/Q3 by low, medium, and high scores on the COCS-N scale. Statistical significance was considered to be indicated by a p-value of less than 0.05. Results: The ANCOVA analysis revealed that three factors were significantly linked to CHWs’ competence. These comprised individual factors: “years of CHWs” (mean ± SD Q1: 6.0 ± 6.0, Q2: 7.8 ± 7.0, Q3: 8.2 ± 7.7, p < 0.001) and “health literacy” (Q1: 27.7 ± 6.6, Q2: 30.4 ± 6.9, Q3: 33.8 ± 7.8, p < 0.001), as well as a community factor: “Sense of community” (Q1: 14.8 ± 3.7, Q2: 16.5 ± 3.5, Q3: 18.2 ± 3.6, p < 0.001). Conclusions: Our finding is that a positive association was derived between COCS-N scores and certain determinants. Notably, “years of CHWs” and “health literacy” in the individual domain, along with the “Sense of community” in the communal context, were firmly established as being significantly associated with CHWs’ competency. Consequently, CHWs need training to increase their “health literacy” and “sense of community”, to acquire high competency in NCD prevention, which will lead to the empowerment of CHWs and maintain their motivation to continue.