Infestation of vegetable fields by the beet cyst nematode, Heterodera schachtii, was first reported in Japan in 2017. After pesticide treatments, fields should be monitored for the possible re-establishment of the nematode population. This paper describes a rapid method of DNA detection by direct extraction of DNA from soil using saturated phosphate buffer, followed by real-time PCR using H. schachtii-specific primers. Accurate handling of many soil samples collected from large fields is possible; however, the method has a limited success rate of one second-stage juvenile (J2) or ten cysts per 10 g of soil, which was determined by adding J2s or cysts in vitro. Using this method on 141 soil samples collected from an infested field, a clear correlation between DNA level and the number of hatched J2s was found. This method enables rapid detection and semi-quantitative measurement of cyst nematodes in the soil.