Commercial mixtures of decabromodiphenyl ether (deca-BDE), a brominated flame retardant, contain not only polybrominated diphenyl ethers (PBDEs, mainly BDE-209) as the main component but also dioxin-like compounds (DLCs) such as polybrominated dibenzofurans (PBDFs). Deca-BDE handling facilities (DHFs) and sewage treatment plants receiving effluent from DHFs are point sources of DLC and flame retardant (FR) pollution. Here, we examined their emission in Japan. For DHF effluents, DLCs detected by the dioxin-responsive chemically activated luciferase expression (DR-CALUX) assay were 1.3−890 pg TCDD-EQ/L (median 46 pg TCDD-EQ/L), while PBDEs and other FRs were <2.0−110,000 ng/L (610 ng/L) and 150− 4,800,000 ng/L (41,000 ng/L). Risk quotients based on predicted no-effect concentrations suggested that DLCs, decabromodiphenyl ethane (DBDPE), tris(2,3-dibromopropyl) isocyanurate (TDBP-TAZTO), and bisphenol A bis(diphenyl phosphate) (BPA-BDPP) present significant risks for aquatic organisms. The concentrations of PBDFs, which are impurities in deca-BDE, were expected to decrease with the inclusion of deca-BDE in the Stockholm Convention list of persistent organic pollutants (May 2017). However, DLCs other than PBDFs and alternative FRs such as DBDPE, TDBP-TAZTO, and BPA-BDPP are likely still discharged. Additional findings indicate that strong (e.g., DLCs, DBDPE, and BPA-BDPP), but not weak (e.g., TDBP-TAZTO), hydrophobic compounds are sufficiently removed by current wastewater treatment processes in Japan.