To investigate important factors affecting the reliability of the analytical results, proficiency tests were attempted for the histochemical method (GUS method) and the qualitative PCR method (PCR method) to detect genetically modified papaya (55-1) in the Japanease official method. The test samples were distributed to twenty-three laboratories that participated in the study and were examined according to the protocol. All the data collected from participating laboratories were statistically analyzed. In the PCR method, one negative sample was detected as positive using detection primers in one laboratory, though the sample was negative when checked using confirmation primers. Contamination might have occurred in the step of the preparation of the PCR sample solution using detection primers. In the GUS method, all the test samples were identified as expected. Thus, all the laboratories reported correct results overall.