Health data from healthcare facilities are helpful to monitoring and planning national health, research in health, healthcare performance, and improvement of patient care. Health data governance is used to increase the benefits of health data and reduce the risk of health data itself. Through the One Data Indonesia program, Indonesia encourages health data quality that the government can use. This research was conducted to analyze the issues in healthcare facilities related to health data governance with a qualitative approach. We used a semi-structured interview with three different healthcare facilities in Jakarta with six participants; hospital director, IT manager, and medical record management. We find five major health data governance issues in healthcare facilities; IT resources and responsibility, data quality, data security, data standard, and policy. It leads to how we should design health data governance in health care to provide high-quality health data for health research, health decision-making, patient care, and national health strategy.