He was questioned for the third successive day on Friday.
The Vatican on Thursday divested Mulakkal, who was the bishop of the Jalandhar diocese of Missionaries of Jesus despite shedding his administrative role, of his pastoral responsibilities "temporarily".
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Silva, who made 53 appearances last season, had his first preseason disrupted by a late start after playing for Portugal in the Confederations Cup.
Claiming innocence, the bishop has said the complaint was "nothing but a fictional story".
The Vatican has accepted a request from a bishop in India to be temporarily relieved of his pastoral duties as police questioned him for a second day over accusations that he raped a nun.
There was no immediate comment from Bishop Franco Mulakkal or his lawyers - though he has denied the charges in interviews in the past.
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Ronaldo scored 44 goals for Real Madrid last season including 15 in the Champions League on the way to a third straight title. Allegri condemned his player after the 2-1 victory, insisting the behaviour was unacceptable.
Following the allegations, dozens of nuns, activists and advocates have protested outside a court demanding his prosecution.
Before he was appointed as the Jalandhar bishop in 2013, Mulakkal served as the auxiliary bishop of Delhi from 2009.
Sankar told reporters on Friday that the police would now investigate charges of rape, illegal confinement, unnatural sex and intimidation. "We are very happy. the Vatican has finally heard our prayers", said one of the nuns. When the church failed to take action on this matter, the nun approached the Kerala police. Mulakkal, who holds a doctorate in moral theology, is the first Indian Catholic bishop to be arrested in a rape case.
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Speaking to the Associated Press , Marion County Coroner Jerry Richardson said, "They're both still under the water". The investigation has been handed over to the South Carolina Law Enforcement Division, the news release said.
The news was welcomed by people in Kochi where nuns of various churches have been protesting for the past ten days. However, the police reportedly submitted an affidavit which states that investigations so far reveal that the bishop had abused his position of power and raped the nun multiple times between 2014 and 2016.