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Disinfection and sterilization against cold-tolerant microorganisms are very important for enhancing food safety and hygiene management under refrigeration conditions. We isolated Exiguobacterium sp. and Pantoea sp. from an immersion solution of packed tofu and evaluated their growth properties and sensitivities to various bactericidal methods. These microorganisms were classified as psychrotrophic bacteria, according to their ability to grow at 4 °C, with an optimum growth temperature of 30 °C. Exiguobacterium sp. and Pantoea sp. were more sensitive to heat and sodium hypochlorite than Escherichia coli (E. coli). Exiguobacterium sp. was sensitive to acetic acid and citric acid, while Pantoea sp. was relatively insensitive and E. coli was insensitive to these organic acids. All microorganisms used in this study were resistant to sodium hydroxide solution (pH 8.00). Exiguobacterium sp. showed resistance to ozonated water and UV; therefore, particular attention should be paid to the contamination of this microorganism in food factories. Both Exiguobacterium sp. and Pantoea sp. were inactivated by pulsed electric field (PEF) treatment that did not cause lethal damage to E. coli. The results obtained in this study suggest that the bactericidal methods targeting the fragile cell membrane with high permeability are effective for the inactivation of cold-tolerant microorganisms.