As a particular institution within the MCD, CTC draws its governance from the Catholic hierarchy of Victoria and Tasmania and three affiliated religious institutes in their desire to provide for the education of clergy and laity in the mission of the Church.
The Senate is the governing body of CTC and comprises the residential bishops of Victoria and Tasmania, the provincials whose seminaries are affiliated with the College, the Master, the Deputy Master, two representatives of the Academic Board, and up to three co-opted members. The Senate meets at least twice a year under the chairmanship of the Archbishop of Melbourne who is the President of the College.

The Academic Board is responsible for the development and implementation of general academic policy regarding teaching and research, within the framework of MCD regulations. The Board consists of the Master, the Heads of Department (philosophy, biblical studies, systematic theology, church history, moral theology and canon law, pastoral and general studies), one other elected academic staff member from each department, the Academic Dean, the Postgraduate Coordinator, and two elected students. The Board may co-opt up to three other members. The Board currently meets five times a year under the chairmanship of the Master.