Since its re-emergence in 1993, the spatial patterns of malaria outbreaks in South Korea have drastically changed. It is well known that complicated interactions between humans, nature, and socio-economic factors lead to a spatial dependency of vivax malaria occurrences. This study investigates the spatial factors determining malaria occurrences in order to understand and control malaria risks in Korea. A multilevel model is applied to simultaneously analyze the variables in different spatial scales, and eigenvector spatial filtering is used to explain the spatial autocorrelation in the malaria occurrence data. The results show that housing costs, average age, rice paddy field ratio, and distance from the demilitarized zone (DMZ) are significant on the level-1 spatial scale; health budget per capita and military base area ratio are significant on the level-2 spatial scale. The results show that the spatially filtered multilevel model provides better analysis results in handling spatial issues.