With the increasing development of genetically modified (GM) crops authorized for use in food, a rapid and accurate method of quantifying the weight-based amount of GM crops is needed to ensure consumers’ rights to choose. Conversion factor (C_f) value is the ratio of the copy number of a GM-specific sequence to an endogenous sequence in the GM crop and is used to convert a copy number ratio of the GM-specific sequence to the endogenous sequence of a sample into weight-based amount of GM crops. However, in the current Japanese official method for GM crops, determining C_f values using real-time PCR instruments capable of rapid measurements has not been established. In this study, C_f values for GM maize and soybean authorized for use as food in Japan were experimentally determined using an Applied Biosystems 7500 Fast Real-Time PCR System, which is capable of rapid measurement. The C_f values were almost the same as those of the PCR instruments described in the Japanese official method, and the weight-based amount of GM maize MON810 measured using this C_f value showed similar results. These results suggest that rapid quantification by this PCR instrument has the same performance as the recommended PCR instruments and may contribute to the labeling regulation of GM crops in Japan.