Flood early warning systems (FEWS) are crucial in reducing flood loss and damage, especially under increasing flood risks due to climate change. Currently, there is limited literature holistically investigating all components of FEWS, namely Risk knowledge, Monitoring and Forecasting, Warning Dissemination, and Preparedness and Response Capabilities. There is also a lack of in-depth understanding of FEWS operation at the local level where local governments play a crucial role. This study conducted a nation-wide survey targeting Japanese municipalities (n = 350) to investigate the current status and challenges of FEWS operations at the local level and the relationships between these elements. The results indicated that while progress in FEWS operation varies in municipalities, they are encountering different challenges in each element of the system. These include a lack of human resources and financial resources, difficulties in risk assessment and data acquisition, limitations of dissemination methods to reach vulnerable, and limited understanding of public perception. This study is the first to investigate all four key elements of FEWS at the local level and the relationships of its key factors, providing useful implications for policy directions to enhance FEWS implementation. All key elements of FEWS positively correlate, suggesting that improving one component can improve the whole system. Government should also strengthen progress in vulnerability assessment, particularly incorporating socio-economic changes as these have the strongest influence on preparedness and response capability of the local areas.