Heat and chemical treatments are commonly employed as decontamination methods in the medical industry. However, there are limitations to these methods, and new decontamination techniques are in demand. Among the state-of-the-art techniques, atmospheric-pressure plasma treatment is considered the most promising approach. Reactive radicals and ultraviolet light, generated in the plasma, are used to kill bacteria located away from the plasma source. In this study, we examined the inactivation of <i>Escherichia coli </i>samples, placed inside a long flexible tube of a small diameter, with plasma jet injection. Depending on the sample position, the inactivation effects of the radicals and ultraviolet light change significantly. Our experimental results show that long-life radicals are effective in plasma treatment. Moreover, the effectiveness of radicals in plasma decontamination was established using mutant gene strains without resistance to specific reactive radicals.