Detection of subjects with oral potentially malignant disorders in a population is key to early detection of oral cancer (OC) with consequent reduction of cancer-related morbidity and mortality. Our aim was to investigate the prevalence and associated risk factors for OPMD in representative provinces of Indonesia. This cross-sectional study was undertaken in five Indonesian provinces: West Java (WJ), Jakarta (JKT), West Papua (WP), West Kalimantan (WK) and Banda Aceh (BA). Respondents answered a previously validated questionnaire including information on ethnicity, occupation, socioeconomic status (SES), oral health practices, and behaviours associated with oral cancer. An oral examination was undertaken using WHO standardized methodology. Data were analysed using ANOVA, Chi-Square, and logistic regression to assess association between risk factors and mucosal disease. A total of 973 respondents between the ages of 17 and 82 years was enrolled (WJ 35.5%,JKT 13.3% WP 18.3%, WK 9%, BA 23.9%). Tobacco smoking (14.8%), Betel quid (BQ) chewing (12.6%) and alcohol drinking (4%) varied geographically. A well-established OPMD was detected in 137 (14.1%) respondents and 2 (0.2%) presented with chronic ulceration later diagnosed as OC. Leukoplakia was the most common OPMD found (9.7%), while the prevalence of oral submucous fibrosis (OSMF), not previously described in the nation, was 2.3%. Poor knowledge of OC risk factors, poor oral hygiene behaviours, low-income SES and ethnicity were significantly associated with the presence of an OPMD. There is a previously under-reported high prevalence of OPMD in Indonesia. Overall, we found a strong correlation between the presence of an OPMD and individual habituation to known risk factors.