(1) Background: A patient safety incident reporting system was introduced in Indonesian hospitals in 2006; however, under-reporting of patient safety incidents is evident. The government plays a vital role in the implementation of a national system. Therefore, this study focuses on how the Indonesian government has been undertaking its role in patient safety at provincial and city/district levels, including incident reporting according to the National Guideline for Hospital Patient Safety. (2) Methods: This study employed a qualitative approach with interviews of 16 participants from seven organizations. The data were managed using NVivo and thematically analyzed. (3) Results: The findings revealed several problems at the macro-, meso-, and micro-level as the government was weak in monitoring and evaluation. The District Health Office (DHO) and Provincial Health Office (PHO) were not involved in incident reporting, and there was a lack of government support for the hospitals. (4) Conclusions: The DHO and PHO have not carried out their roles related to patient safety as mentioned in the national guidelines. Lack of commitment to and priority of patient safety, the complexity of the bureaucratic structure, and a lack of systematic partnership and collaboration are problems that need to be addressed by systematic improvement. To ensure effective and efficient national outcomes, the three levels of government need to work more closely.