We examined variations in dengue vector control costs and resource consumption between the District Health Departments (DHDs) and Local Authorities (LAs) to assist informed decision making as to the future roles of these agencies in the delivery of dengue vector control services in Malaysia. Data were collected from the vector control units of DHDs and LAs in 8 selected districts. We captured costs and resource consumption in 2010 for premise inspection for mosquito breeding sites, fogging to destroy adult mosquitoes and larviciding of potential breeding sites. Overall, DHDs spent US$5.62 million or US$679 per case and LAs spent US$2.61 million or US$499 per case. The highest expenditure for both agencies was for fogging, 51.0% and 45.8% of costs for DHDs and LAs, respectively. The DHDs had higher resource costs for human personnel, vehicles, pesticides, and equipment. The findings provide some evidence to rationalize delivery of dengue vector control services in Malaysia.