The aim of this study is to examine the challenges of using the system of Hamanandjoo and the existing rules in Iranian universities for using this system and protecting scientific integrity in Iranian higher education. Taking into account their basic assumptions and the facilities available and used by universities in implementing the rules, the study focuses on three main contexts: Research ethics; scientific integrity; and Hamanandjoo system. The findings show that the scientific integrity of commitment to discover, publish and establish the truth is not achieved solely by relying on the Hamanandjoo system. Furthermore, the use of this system as the exclusive source for the establishment of scientific integrity leads to results that are contrary to expectations and also to the goals for which the system has been established. Thus, the study shows how the rules of universities for using the system lead to a legal action to reverse the criteria of scientific integrity.