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The University is being accused by Pastor Martin Ssempa, of refusing to allocate him land on campus to build a fully-fledged church as is the case with other religions.
The university, however, insists it can only accommodate three mainstream religions on campus, namely the Catholics, Anglicans, and Muslims.
In his petition before the EOC, Pastor Ssempa says by refusing to gazette the Born Again Pentecostal religion, the university is discriminating against a significant number of students who subscribe to the religion.
The pastor as such wants the Commission to order Makerere to allocate him land to construct a church and a house for the chaplain.
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"The university needs to move very fast because it is opening in August and yet the chaplaincy has not yet been granted. This is denying the born-again faith ability to provide spiritual formation of born-again students who are discriminated against compared to other faiths in the university," Ssempa told the Commission in his petition.
Makerere University was summoned last week by the Commission to file its response in the case.
For years, Pastor Sempa has been running the Makerere Community Church (MCC) in a lecture room at one of the colleges.
He has also been conducting the famous weekly Prime Time sermons at the University Pool.