The COVID-19 pandemic witnessed a surge in the use of health data to combat the public health threat. As a result, the use of digital technologies for epidemic surveillance showed great potential to collect vast volumes of data, and thereby respond more effectively to the healthcare challenges. However, the deployment of these technologies raised legitimate concerns over risks to individual privacy. While the ethical and governance debate focused primarily on these concerns, other relevant issues remained in the shadows. Leveraging examples from the COVID-19 pandemic, this perspective article aims to investigate these overlooked issues and their ethical implications. Accordingly, we explore the problem of the digital divide, the role played by tech companies in the public health domain and their power dynamics with the government and public research sector, and the re-use of personal data, especially in the absence of adequate public involvement. Even if individual privacy is ensured, failure to properly engage with these other issues will result in digital epidemiology tools that undermine equity, fairness, public trust, just distribution of benefits, autonomy, and minimization of group harm. On the contrary, a better understanding of these issues, a broader ethical and data governance approach, and meaningful public engagement will encourage adoption of these technologies and the use of personal data for public health research, thus increasing their power to tackle epidemics.