The national security issues in particular non-traditional security issues such as law enforcement, health, food, supply chain management, industry etc. are severely impacted by the COVID-19 outbreak in all countries of the world. As such, the developing country like Indonesia has largely been suffering from this epidemic. In this context, this paper attempts to analyse some national security issues that are affecting Indonesia, which is currently struggling with the COVID-19 pandemic. Proposed here are policy measures to combat both present and future challenges. The study uses secondary data collected from different sources concerning COVID-19 pandemic and security issues of Indonesia. The study analyses the data based on descriptive statistics, highlighting the impact of the COVID-19 pandemic on Indonesian law enforcement issues, and security of health, food, supply chain management, industrial and other economic sectors. The study argues that if the vulnerability continues in these security-related issues due to pandemic, the country will face a harsh reality to manage the state-affairs. Therefore, the policy options are mainly concerned with the COVID-19 issue. Indonesia’s government should identify what measures to take by conducting rapid diagnostics and polymerase chain reaction tests in the laboratory, respectively. Moreover, the government and relevant stakeholders need to develop strategies that break the stranglehold of COVID-19 transmission in order to resolve Indonesian national security concern.