Chlorination in sewage treatment induces a large portion of bacteria to the viable-but-non-culturable (VBNC) state, in which bacteria remain viable and metabolically active but unable to reproduce on culture media. Disinfection outcomes are monitored by estimating the concentrations of culturable faecal indicator bacteria (FIB). Previous studies have shown the presence and proportions of VBNC FIB before and after chlorine disinfection in two effluent types in Hong Kong. However, little is known about the relationships between the disinfection medium, chlorine dosing regime and the induction of VBNC states in the FIB. We conducted microcosm experiments of chlorine disinfection on Escherichia coli and Enterococcus faecium in phosphate-buffered saline (PBS) as a baseline study prior to future testing using sterile sewage. The results showed that chlorination effectively reduced culturable plate counts to meet effluent discharge standards. Yet, a large number of cells were still detected as viable by flow cytometry. Transcriptomic analysis of the VBNC states of the FIB in PBS and sterile sewage revealed distinct strategies employed by E. coli and E. faecium to counteract chlorine stress, including alterations in metabolic pathways and transport activities. The induction of VBNC state in the FIB could lead to a false impression of sufficient disinfection, as VBNC bacteria in disinfected sewage effluents may resuscitate upon discharge into receiving marine waters. As the concentration of viable FIB has been underestimated, the risk assessment of the impacts of effluent discharges to public and ecosystem health in the receiving marine environment would be inaccurate. These findings in this study enhance our understanding of the physiological responses of FIB in the chlorine-induced VBNC states, provide insights for the optimization of disinfection processes and improve the accuracy in risk assessment for effluent discharges into receiving waters.