Drinking water disinfection techniques without the dosage of chemicals are regarded as more advantageous in terms of costs and practical use. Here we investigated the efficacy of electrochemical disinfection for inactivation of Bacillus subtilis spores – a model microorganism of highly resistant pathogens. The effect of electrochemical disinfection with TinO2n−1 ceramic electrodes which generate active chlorine from chloride in situ, was compared to the traditional chlorination in which active chlorine was produced from addition of sodium hypochlorite. Research was performed on a batch scale with a synthetic buffered drinking water containing 35.5 mg/l of chloride ions. Spore viability was analysed with both cultivation and cell potential for dividing (direct viable count method). The results showed that at similar residual disinfectant concentrations x contact time (CT value), electrochemical disinfection was over three times more effective in neutralizing both cultivable B. subtilis spores and those with cell potential for dividing than traditional chlorination. As in chlorination, electrochemical disinfection was shown to be water-pH dependent and the lowest CT value of 112 mg/l min−1 (2-log removal) was obtained at pH 6. The lowest efficiency for both techniques was observed at pH 8. In conclusion, electrochemical disinfection is a viable in situ method even at low levels of chlorides in drinking water and appears to be more effective than simple chlorination with the addition of the active chlorine species when highly resistant microbial forms are analysed, however, to apply the technology on a large scale additional studies on potential formation of disinfection by-products must be performed.