This paper demonstrates the effect of ferrate [Fe(VI)-compound], an environmental friendly multi-purpose reagent, in municipal secondary effluent treatment. The purpose was to study the inactivation capability of ferrate and for the first time to compare the effect and efficiency of Fe(VI) with the widely used disinfectant, chlorine gas on the indigenous bacterial community in the case of secondary effluents. The most probable number technique (MPN) was applied for the determination of cultivable heterotrophic bacterial abundance and terminal restriction fragment length polymorphism (T-RFLP) analysis for comparing bacterial communities. The study demonstrated that (i) ferrate and chlorine had different effect on the total bacterial community of secondary effluents, (ii) low ferrate dose [5 mg L-1 Fe(VI)] was sufficient for >99.9% reduction of indigenous bacteria, and (iii) a similar dosage was also effective in the inactivation of chlorine-resistant bacteria. (C) 2011 Elsevier Ltd. All rights reserved.