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Contaminants are efficiently purified without affecting the environment or necessitating the performance of any post-treatments such as pH adjustment that would be used to prevent environmental impact, even when the contaminated soil is highly viscous. In the method of purifying contaminated soil by microorganisms according to the present invention, contaminated soil mainly comprising clay or silt and containing trichloroethylene as a contaminant is dug out, and then temporarily placed on the ground (step 101). Next, perlite 2, which is an inorganic soil-improving material, the soil-improving material, and degradation microbes 3 degrading trichloroethylene are added to the contaminated soil 1 (step 102). The contaminated soil is subsequently mixed by agitation, so as to cause the perlite 2 to absorb pore water contained in the clay or silt (step 103). Next, aeration is performed to inject air into the contaminated soil 1, thereby microbially degrading trichloroethylene (step 104).