The invention comprises a proton beam positioning method and apparatus used in conjunction with multi-axis charged particle radiation therapy of cancerous tumors. The proton beam verification system allows for monitoring of the actual proton beam position in real-time without destruction of the proton beam. The system includes a coating or thin layer substantially in contact with a foil covering the end of an exit nozzle or is a layer located after the x- and y-axis proton beam scanning controllers and before the patient. The coating yields a measurable spectroscopic response, spatially viewable by the detector, as a result of transmission by the proton beam. The proton beam position is monitored by the detector and compared to the calibration and/or treatment plan to verify accurate proton delivery to the tumor and/or as a proton beam shutoff safety indicator.