Indonesia is the biggest archipelago in the world with large water areas. Indonesia produces and consumes a high amount of fishery products. However, there is a heightened risk of heavy metal contaminants in those products as heavy metals are accumulated along the aquatic food chain. In this review, the concentration of heavy metals, mainly arsenic, cadmium, mercury, and lead, in fish and fish products acquired in Indonesia were discussed. Those heavy metals are toxic at low levels and their concentrations in fish and fish products are regulated by the National Agency of Drug and Food. In some polluted areas, such as Ciliwung River (Jakarta and West Java), Donan River (Central Java), and Jakarta Bay, the content of heavy metals in fish were above the permitted threshold. Surveillance of the heavy metal concentrations in fish and fish products by the National Agency of Drug and Food has been implemented but a more frequent and thorough inspection is needed. Moreover, fishing should be discouraged in highly polluted areas by the local government to avoid the consumption of contaminated aquatic animal products.