There were 396 (80%) out of 495 malaria-endemic districts/cities in Indonesia in 2007 leading to the issuance of Health Ministerial Decree No. 293 in the year 2009 on malaria elimination. Therefore, the study was needed to determine the inter-sector roles to support malaria elimination in Riau Islands. The study was an observational study with a cross sectional design. Data were collected through focus group discussions involving institutions, such as the Regional Development Planning Agency, Office of Public Works, Office of Environmental Affairs, Office of Marine and Fisheries, and private sectors. Data were analyzed by content analysis. The results revealed that roles of key stakeholders were determined. For instance, drainage constructions by the Office of Public Works led water flow or eliminated pools for malaria vectors breeding. The Office of Environment Affairs restored such environmental conditions to avoid Anopheles mosquitoes breeding places. The Office of Marine and Fisheries reared certain fish as predators of the Anopheles to stop malaria transmission. Under decentralization, roles of the Local Government or District Secretary is required to synergize the inter-sector collaboration. Collaboration between local governments and private sectors should be enhanced through Environmental Impact Assessment for broad and healthy environmental development.