The study aimed to determine the extent of implementation of the Clinical Supervision Program and the level of teachers’ instructional competence based on COT–RPMS ratings. It also sought to establish a relationship between the extent of implementation of the Clinical Supervision Program and the level of teachers’ instructional competence based on COT–RPMS ratings, as well as to identify the challenges encountered by teachers in the clinical supervision process. A descriptive-correlational research design was employed covering all the schools in Diffun District I with 142 teacher-respondents. Findings revealed that the clinical supervision program is strongly perceived by teachers as effectively implemented across its three phases: pre-observation conference, classroom observation, and post-observation feedback, each fostering clear communication, collaboration, and professional growth. Moreover, teachers demonstrated outstanding instructional competence. Furthermore, the extent of clinical supervision implementation is not significantly correlated with teachers’ instructional competence, indicating other factors may influence competence beyond supervision perception. Meanwhile, teachers encountered several challenges in the clinical supervision process, including limited time for pre-observation conferences, unclear communication of objectives and criteria, insufficient involvement in planning observations, anxiety during observations, and feedback that is often too general or delayed. These findings highlight that clinical supervision can be improved through clear communication, collaborative planning, and constructive feedback, addressing time and involvement challenges, supporting supervisors, integrating professional development, monitoring progress with COT–RPMS, and fostering reflective practice to enhance teacher growth and student outcomes.