Indonesia is the world largest producer of the red seaweeds Kappaphycus and Eucheuma; however, this country is facing significant challenges such as disease outbreaks, epiphyte infestations and a loss in seedling quality. Biosecurity practices have been widely adopted in other aquaculture sectors and when enforced can help to limit the introduction and spread of diseases and pests. To assess current capacity for biosecurity in seaweed aquaculture in Indonesia, a systematic analysis of policy frameworks including legislation, regulatory tools, and national standards was conducted. Biosecurity themes and risks were used to evaluate current national biosecurity content. The results identified major challenges faced by the industry in order to implement biosecurity policies in practice. Barriers to implementation included unspecific reference to the seaweed aquaculture sector, limited variety of approaches to biosecurity, limited use of up-to-date scientific evidence, insufficient guidance for the use of precaution and insufficient inclusion of specific biosecurity hazards. In general, although national regulations are currently under revision, current policies indicate a lack of clarity where biosecurity is included. Six recommendations are suggested to incorporate proactive biosecurity actions into current frameworks, with the aim of improving the health and sustainability of the seaweed aquaculture sector in Indonesia.