To provide a radiation image processing system, a program, and a defective pixel correcting method which are capable of accurately correcting defective pixels even if a defect due to a pixel defect of a TFT active matrix substrate and a defect due to scratches of a scintillator or mixture of chips are mixedly present at the same position.

A CPU 58A acquires a specific defective pixel obtained by removing a second defective pixel, from a first defective pixel; the first defective pixel being indicated by a first defective map for indicating the position of the first defective pixel in a radiation image picked up by irradiating an imaging region with a radiant ray by a radiation detector 20 of an indirect conversion system, the second defective pixel being indicated by a second defective map for indicating the position of the second defective pixel in a radiation image picked up without irradiation with a radiant ray by the radiation detector 20. Regarding the acquired specific defective pixel, defective pixel correction is applied to a radiation image picked up by the radiation detector 20, including at least some peripheral pixels as a correction target.