Many restricted data managing organizations across the world have adapted the Five Safes framework (safe data, safe projects, safe people, safe setting, safe output) for their management of restricted and confidential data. While the Five Safes have been well integrated throughout the data life cycle, organizations observe several unintended challenges regarding data being FAIR (Findable, Accessible, Interoperable, Reusable). In the current study, we review the current practice on the restricted data management and discuss challenges and future directions, especially focusing on data use agreements, disclosure risks review, and training. In the future, restricted data managing organizations may need to proactively take into consideration reducing inequalities in access to scientific development, preventing unethical use of data in their management of restricted and confidential data, and managing various types of data.