BackgroundGeographical variation may likely influence the effectiveness of prevention efforts for malaria across Indonesia, in addition to factors at the individual level, household level, and contextual factors. This study aimed to describe preventive practices at individual and a household levels applied by rural communities in five provinces in eastern Indonesia and its association with the incidence of malaria among adult (≥15 years) populations.MethodsThis study analyzed a subset of data of nationally representative community-based survey 2018 Riset Kesehatan Dasar (Riskesdas). Data for socio-demographic (age, gender, education and occupation) and preventive behaviors (use of mosquito bed nets while slept, insecticide-treated mosquito nets (ITNs), mosquito repellent, mosquito electric rackets, mosquito coil/electric anti-mosquito mats, and mosquito window screen) were collected. Data were analyzed using bivariate and multivariable logistic regression model.ResultsTotal of 56,159 respondents (n = 23,070 households) living in rural areas in Maluku (n = 8044), North Maluku (n = 7356), East Nusa Tenggara (n = 23,254), West Papua (n = 5759) and Papua (n = 11,746) were included in the study. In the multivariable models, using a bed net while slept likely reduced the odds of self-reported malaria among Maluku participants. Reduced odds ratios of self-reported malaria were identified in those participants who used ITNs (North Maluku, ENT, Papua), repellent (Maluku, West Papua, Papua), anti-mosquito racket (ENT), coil (Maluku, North Maluku, Papua) and window screen (West Papua, Papua).ConclusionOur study concluded that the protective effects of preventive practices were varied among localities, suggesting the need for specific intervention programs.