ObjectivesThis study aims to investigate ethnic variation and its association with malaria awareness in the East Nusa Tenggara Province (ENTP), Indonesia.MethodsA community-based cross-sectional study was conducted upon 1495 adults recruited by multi-stage cluster random sampling technique. A malaria awareness related questionnaire was used to collect data alongside a malaria awareness index (MAI). A logistic regression method was applied to quantify the strength of associations of factors associated with the awareness index.ResultsOf total participants, 33% were from Manggarai, 32.3% were from Atoni, 30.2% from Sumba ethnicity. The level of MAI was significantly different between these groups with the highest in Manggarai ethnicity (65.1%, 95% confidence interval (CI): 59.9 – 70.3) and the lowest in Sumba ethnicity (35%, 95% CI: 27.6 – 42.4). The most prominent factors influencing the MAI in Sumba and Manggarai ethnicity were education level, whilst it was socio-economic status (SES) in Atoni ethnicity. The level of MAI was significantly higher for adults with diploma or above education level (adjusted odds ratio (AOR): 21.4, 95% CI: 3.59 – 127.7-for Manggarai ; AOR: 6.94, 95% CI: 1.81 – 26.6 for Sumba). The level of MAI was significantly higher for adults living in high SES in Atoni (AOR 24.48, 95% CI: 8.79 – 68.21).ConclusionsPoorer education levels and low SES were more prominent factors contributing to lower levels of MAI in rural ENTP. Interventions should focus on improving malaria awareness to these groups to support the national commitment of the Indonesian government to achieve malaria elimination zone by 2030.