This study assesses radiation doses in cone beam computed tomography (CBCT) procedures in Sri Lanka, with the goal of establishing initial diagnostic reference levels (DRLs). Data from 1162 retrospective scans across four institutions were analyzed, and the medians of the pooled dose distribution for seven clinical indication categories were presented as the DRL values. The proposed DRLs based on clinical indications are 1013 mGy·cm2 for pathological conditions including cysts, tumors, and lesions, 1307 mGy·cm2 for implant planning, 1266 mGy·cm2 for presurgery assessment, and 1585 mGy·cm2 for evaluation of sinus and nasal pathology, temporomandibular disorder, and facial trauma. Considerable variability in doses across facilities was observed, driven by differences in equipment and imaging practices. Therefore, this study recommends adopting suggested DRL values as benchmarks, standardizing protocols to reduce dose variability, and implementing a national framework for regular updates of DRL values.