Church sources said a five-member Episcopal council led by senior metropolitan Kuriakose Mar Cleemis would manage administration of the church till October 14.
The long-standing feud between Jacobite and Orthodox Church factions is a hot topic for political debate that comes alive every poll season in the state.
Last month, a man from Pathanamthitta district accused five priests of the Malankara Orthodox Syrian Church in Kerala of using his wife's secret confession to blackmail and sexually abuse her.
Representatives of the Kerala Church Act Action Council who stand for reforms in the Church said there was a possibility of intimate confessions by women being "misused" in the present form.
Five priests have been directed to keep away from their official duties following a complaint from a believer alleging they have been blackmailing his wife for sexual favours.