Membrane bioreactor (MBR) process is superior to the conventional activated sludge (CAS) process in many aspects of wastewater treatment, and it is expected to perform better in terms of virus removal compared to CAS. However, the virus concentration in MBR-treated wastewater often falls below the limit of detection (LOD), making it difficult to measure with conventional detection techniques. In this study, we modified the efficient and practical virus identification system with enhanced sensitivity for membrane (EPISENS-M) method, originally developed for raw sewage, to a low-concentration version applicable to MBR-treated wastewater. We could successfully lowered the LOD to 0.1 copies/L. This improved method demonstrated the ability to quantify pathogenic viruses in effluents from an MBR treating municipal wastewater with approximately 100 to 1000 times the sensitivity of traditional detection techniques. Additionally, the virus removal rates calculated from the measured values showed a log reduction of 4 log₁₀ or higher for each virus, significantly higher than that of CAS. The modified EPISENS-M method for low-concentration ranges is useful for quantitatively evaluating the virus removal performance of MBR systems.