El Niño events typically lead to delayed rainfall and decreased rice planting in Indonesia's main rice-growing regions, thus prolonging the hungry season and increasing the risk of annual rice deficits. Here we use a risk assessment framework to examine the potential impact of El Niño events and natural variability on rice agriculture in 2050 under conditions of climate change, with a focus on two main rice-producing areas: Java and Bali. We select a 30-day delay in monsoon onset as a threshold beyond which significant impact on the country's rice economy is likely to occur. To project the future probability of monsoon delay and changes in the annual cycle of rainfall, we use output from the Intergovernmental Panel on Climate Change AR4 suite of climate models, forced by increasing greenhouse gases, and scale it to the regional level by using empirical downscaling models. Our results reveal a marked increase in the probability of a 30-day delay in monsoon onset in 2050, as a result of changes in the mean climate, from 9-18% today (depending on the region) to 30-40% at the upper tail of the distribution. Predictions of the annual cycle of precipitation suggest an increase in precipitation later in the crop year (April-June) of approximately 10% but a substantial decrease (up to 75% at the tail) in precipitation later in the dry season (July-September). These results indicate a need for adaptation strategies in Indonesian rice agriculture, including increased investments in water storage, drought-tolerant crops, crop diversification, and early warning systems.