The accused clergy member is Bishop Franco Mulakkal of the Jalandhar diocese.
The nun claims she was raped multiple times by him between 2014 and 2016. She had written a 7-page letter to the Vatican after frustration with the local police and church.
Five nuns had also protested outside the High Court in Kerala, demanding the Bishop be arrested.
Both the accused and accuser are from the Missionaries of Jesus church, who initially defended the Bishop in a statement and said the nun was conspiring against him.
The police have now issued a summons for him on the 19th September and the church have said they will have a one-member panel investigation and he has stood down.
The Bishop said in a statement: "as you have probably come to know from the media the investigation into the allegations raised against me as there are several contradictions in the evidences collected against me as per the report of the police and it is reported that I am likely to be called for further clarifications by the investigating officer in Kerala. In my absence Msgr. Mathew Kokkandam will administer the diocese as in the normal practice when I am away from the diocese".
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