Objective: PET images are affected by scanner model, reconstruction conditions, injected dose, scan duration, patient health status and FDG radiopharmaceutical supply systems. The present study compares images of 40 patients using commercial and in-house FDG systems with one PET scanner (Aquiduo). Methods: The PET images were evaluated using the physical indexes of NEC_patient, NEC_density and SNR_liver proposed by the Japanese guidelines for oncological FDG-PET/CT, and by visual assessment. Results: There were no significant differences in the physical indexes between PET images generated using commercial and in-house FDG. The physical indexes were also acceptable according to the recommended Japanese guidelines. NEC_density was higher when a higher dose/body weight of commercial FDG was injected (correlation coefficient: r=0.576, p<0.001) and lower when BMI was lower and in-house FDG was injected (r=−0.786, p<0.0001). These results suggest that scan duration should be increased if the injected dose of commercial FDG/body weight is <5.5 MBq/kg, and if individuals with BMI >21.4 kg/m² are injected with in-house FDG. Conclusions: Scan duration should be varied depending on FDG supply systems to ensure more accurate image quality and quantitative values during evaluations of response to therapy and prognostic prediction.