Air conditioning systems consume almost 40% of energy in buildings. They contribute to global warming both indirectly from their fossil fuel use of electricity and directly through their refrigerant releases. The use of natural refrigerants reduces energy consumption and GHG emission, however, their flammability poses risk in their implementation. This paper discusses the risk assessment of flammable refrigerant applications in air conditioning systems in Indonesia. There are two main hazards in the application: fire and explosion. A semi-quantitative risk assessment is performed. The study combines primary data from accident reports in transportation, installation, operation, service and maintenance of air conditioning systems with flammable refrigerants. A case study of risk assessment in an air-cooled chiller with a refrigerant leakage scenario using computational fluid dynamics is presented. The results indicate that significantly high risk occurs during service and maintenance activity, while lower risk occurs during operation. Several risk mitigation and reduction efforts are recommended that include technical and regulatory approaches.