Bishop Franco Mulakkal, who maintains his innocence, will be charged and face trial by a special prosecutor on accusations of rape and intimidation, police said.
He was arrested on 21 September in the southern state of Kerala on suspicion of raping the nun 13 times between 2014 and 2016.
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She first spoke out in June but police started formal questioning only in September as fury over the case mounted.
The church acknowledged the accusations only after five of the woman’s fellow nuns mutinied and publicly rallied to her side to draw attention to her year-long quest for justice, despite what they described as heavy pressure to remain silent.
“We used to see the fathers of the church as equivalent to God, but not any more,” one of the nuns from the convent said.
“How can I tell my son about this, that the person teaching us the difference between right and wrong gave him his First Communion after committing such a terrible sin?”
The case is part of a larger problem in the church that Pope Francis addressed on Tuesday for the first time after decades of silence from the Vatican. He acknowledged that sexual abuse of nuns by clerics was a continuing problem.
At a time when church attendance is low in the West, and monasteries are being closed across Europe and America, the Vatican increasingly relies on places such as India to keep the faith growing.
“If this case goes ahead, it will be a new beginning, and priests and bishops will be forced to be held accountable,” said the Reverend Augustine Vattoly.
The reverend said he was an early supporter of the nun’s accusations and was ordered by his superiors to back away or face repercussions.
“The church is losing its moral authority,” Reverend Vattoly added.
New York Times