Indonesia is a developing country in the South East Asian region (SEAR), with a total population of 237,641,326, in 2010, living in 33 provinces. In line with economic development and decentralisation of the health system, the number of health care establishments steadily increases to keep up with population growth and public needs. Institutions delivering health services, including hospitals and health centres (HCs), inevitably generate a tremendous amount of wastes, a fraction of which are infectious and hazardous. The majority of health care institutions do not manage their medical wastes, properly, to minimise their risks. Consequently, their wastes are unsafe for patients, health care workers, waste handlers and the general population. These can spread health care-acquired infections (HAI). The Government of Indonesia (GoI) enacted a number of laws and regulations to govern the implementation of sound environmental management, municipal solid waste management (MSWM), and hazardous waste management. However, there is no clear policy framework to ensure safe health care waste management (HCWM), in accordance with such laws and regulations. A cross-sectional study was carried out in 2010 to develop a suitable policy framework for sustainable HCWM. It employed concurrent mixed methods, including quantitative and qualitative inquiries, consisting of mailed survey questionnaires and in-depth interviews, waste audits and onsite observations. The mailed survey, using a structured questionnaire, reached 237 sample public hospitals across 27 provinces. In-depth interviews with relevant policy makers were conducted in eight hospitals, five HCs from five provinces, and four institutions at the central level, including the Ministries of Health (MoH), and Environment (MoE), as key stakeholders. The waste in eight large hospitals across five provinces was audited.