The principle of judicial authority—which asserts that in criminal matters, the intervention of a competent authority is necessary for prosecution and investigation, and that only a competent authority can issue and execute sentences—is one of the most fundamental indicators of a fair trial. Weakening this principle also challenges the principle of legality and the rule of law. The challenges to the principle of judicial authority, irrespective of their diversity and quality in different criminal policy systems, are partly related to the personal preferences of judges and confirmation biases in judicial positions, and partly due to the inefficiency of the judicial system in controlling factors that weaken this principle. In this study, the challenges to the principle of judicial authority in Iran's criminal policy are examined in two parts: judges' personal preferences and the inefficiency of the judicial institution. In the section on judges' personal preferences, issues such as religion, race, gender, and political affiliation are discussed. In the section on the inefficiency of the judicial institution, factors like the reduction of the elite pool of judges, caseload pressures, managerialism, and concerns related to the economic welfare of judicial employees are highlighted. The research findings indicate that the challenges to the principle of judicial authority are not specific to any particular criminal policy system. However, the important point is that each criminal policy system can overcome these challenges through scientific and effective methods utilizing the indigenous capacities of its criminal policy.