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The charge sheet was filed in a magistrate court at Pala in the district.
Mulakkal was former Bishop of Jalandhar diocese and a senior member of the Roman Catholic clergy in India.
The nun, who belongs to Missionaries of Jesus congregation under Jalandhar diocese, had accused the 55-year-old clergyman of repeatedly raping and having unnatural sex with her between 2014 and 2016.
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He has been charged under various sections of the Indian Penal Code including 342 (punishment for wrongful confinement), 376C (sexual intercourse by person in authority), section 377 (unnatural sex) and 506(1) (criminal threat), official sources said.
In her complaint to police in June, the nun had alleged that Mulakkal raped her at a guest house in Kuravilangad in May 2014 and later sexually exploited her on several occasions.
She said she had to approach police as the church authorities did not act on her repeated complaints against the clergyman.
Mulakkal, however, has claimed that he was “absolutely innocent” and “falsely implicated” with an “ulterior motive and vexatious intention”.
Five nuns, who led a public protest seeking Mulakkal’s arrest, welcomed the police’s decision to file charge sheet in the case and said they were satisfied with the investigation.
They expressed hope that the accused Bishop will get maximum punishment in the case.
According to sources, the charge sheet included 83 witnesses including top clergymen of the Catholic church.
Ahead of his interrogation and arrest, the Vatican had relieved him “temporarily” of all pastoral responsibilities as the bishop of the Jalandhar Diocese.
Mulakkal was arrested in September last amid mounting public outrage over allegations of repeatedly raping and sexually assaulting the nun.
He was released from a sub-jail in Pala on October 16 after the Kerala High Court granted him bail.