High-energy low-mass proton implantation achieved considerable interest in semiconductor technology, due to much deeper penetration of hydrogen ions into silicon as compared to common dopants, boron, phosphorous, and arsenic. Accordingly, monitoring the accumulation kinetics and stability of proton-implantation induced defects and their influence on the optical and electrical properties of Si achieved increased attention both in technological process control and scientific research. We show that photo-modulated-reflectance (PMR) is effective technique to measure very low defect concentrations in the ppb-ppm range in high energy proton implanted silicon. After ion irradiation, the as-implanted dilute damage structure may lead to long term changes of the defect distribution and the formation of defect compounds due to mobility of point defects at room temperature. Moreover, low-mass hydrogen atoms may move significantly faster at room temperature compared to heavier dopants. We show that PMR is capable to detect differences in implanted proton dose with high sensitivity in a wide dose range, and, on a longer time scale, allows to follow changes in free carrier generation and recombination processes through the measurement of the long term decay of the PMR signal which is related to the sample response based on electro-optic and thermo-optic effects. Our experiments may pave the way toward high precision process control of device structure fabrication which utilizes the high-energy hydrogen implantation step. Also, our aim is to gain insight into the main processes underlying the dose dependent change and long-term decay of the PMR signal in high energy proton implanted Si.