Bishop Franco Mulakkal was arrested in southern Kerala state on Friday after Pope Francis relieved him from duty over the scandal that has sparked days of angry protests by clergy over police inaction.
Mulakkal, who heads the Roman Catholic diocese of Jalandhar in the northern state of Punjab, is accused of raping the nun 13 times between 2014 and 2016.
The nun, who has not been named, first accused Mulakkal in June but police only started formal questioning this month as fury over the case mounted.
Police asked for more time on Saturday to question the 52-year-old, who has denied the accusations.
In its submission to the court in Kerala, police said Mulakkal had illegally confined the victim in a guesthouse and subjected her "to rape and unnatural sex 13 times in the same room," the Times of India newspaper reported.
Mulakkal has called the scandal a conspiracy by those opposed to the Roman Catholic Church.
The Catholics Bishops' Conference of India has said Mulakkal's arrest was a "sad moment for all of us".
"As said before we expect the law to take its course and for the truth to emerge. At his moment our prayer is for healing," it said in a statement Friday.
Sexual abuse by clergy and the failure of Church officials to take action has been one of the biggest scandals facing Roman Catholicism globally in recent years.
Recently five priests from Kerala, home to India's largest Christian population, were arrested after sexual assault allegations.
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