The practices of the Ministry of Religion in Indonesia that discriminates against and disregards the freedom and rights of the minority are contradictory to the aspirations of the founding fathers of the nation as declared in the Indonesian Constitution. In order to bridge this gap it is essential to have a critical and reflective study on religion-state relations and the existence of the Ministry of Religion. The study presented in this article will deal with this problem from a historical standpoint and will be based on the underlying principles of Christian witness and thought in Indonesia. It will also recommend some practical strategies in protecting the freedom and rights of the minority in Indonesia.