Franco Mulakkal was charged with raping the nun several times between 2014 and 2016, police deputy superintendent of Vaikom district, K. Subash, told AFP.
The bishop faces other charges including unlawful detention, unnatural sex and abuse of authority. Facing a maximum punishment of life imprisonment, Mulakkal has denied the allegations.
Vatican suspends Indian bishop accused of raping nun
Local media said the report backing the charges ran into more than 100 pages and contained testimonies from priests, bishops and nuns.
The victim filed a formal complaint in June last year, but police only started formal questioning in September after fury over the case mounted.
The lack of action provoked outrage and five nuns — in a rare public show of dissent within the church — staged days of protests with dozens of supporters.
Mulakkal was arrested in October before being released on bail. Senior members of the church in the southern state have supported the 55-year-old bishop, however, and he was cheered when he returned to his diocese.
Indian bishop granted bail in nun rape case
Christians — overwhelmingly Catholic — are the third-largest religious group in India. Around 80 per cent of the country's 1.3 billion population is Hindu, followed by a sizeable Muslim minority.
Sexual abuse by clergy and the failure to take action has mired the Roman Catholic Church in scandal across the world in recent years.
In February, Pope Francis publicly addressed sexual abuse of nuns by clerics for the first time, insisting the Vatican takes seriously reports of sexual abuse and the "sexual slavery" of nuns.
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