In this paper, FDI Research Analyst Jarryd de Haan examines some of the primary internal security threats facing Indonesia: terrorism and extremism, separatism, ethnic and religious violence, and piracy. Of those threats, Mr de Haan notes that terrorism and piracy represent the most immediate concerns for the Indonesian Government. Separatism and ethnic and religious violence, on the other hand, could be significant challenges in the long term, especially if other factors, such as an economic crisis, take effect.
The paper can also be downloaded here.