Indonesian food products need to comply with halal regulations, including the ones from fisheries-based agro-industry. The absence of halal certificates will limit the market and consequently will lead to the risk of lower productivity performance. This study aims to identify sources of risk in the fisheries agro-industry based on Indonesia’s Halal Assurance System called Sistem Jaminan Produk Halal (SJPH). It conducts risk assessments and develops strategies to increase the productivity performance of the industry based on the identified risks. The criteria considered in the risk identification including commitment and responsibility, raw material, production process, final product as well as monitoring and evaluation. The research used Failure Mode Effect Analysis (FMEA). The data was collected through observation, interviews, and questionnaires. All identified risks were then evaluated and eliminated based on the Risk Priority Number (RPN). The research was conducted on ten fisheries-based agro-industries in the Sidoarjo Regency, East Java, Indonesia. The study shows that there are 22 sources of risk, with the highest-ranked one is training activity. The recommended strategy to increase the halal-based productivity performance is strengthening the commitment of all involved stakeholders, increasing human resources' knowledge, improving facilities and infrastructure as well as strengthening monitoring and evaluation using management information systems.