A group of nuns, led by Sister Anupama, had fought on behalf of the victim nun who had accused Mulakkal of raping her multiple times.
The Kerala Police on Monday registered a case against Catholic Bishop Joseph Kallarangatt on the basis of a complaint that the priest through his "love and narcotic jihad" remarks, committed the offence of promoting feelings of hatred between different groups on the grounds of religion.
Nuns doubt Bishop Franco still wields power in the diocese.
A group of nuns of Kuravilangad convent in Kottayam district of Kerala, who have been standing with the survivor in her fight, were on the verge of tears when they said they were yet to believe such a verdict came out from the court and they did not know what has happened.
They alleged that the police probing the case was trying to sabotage the investigation.
Bishop Mulakkal, a senior member of the Roman Catholic clergy in India, was arrested last year following allegations by the nun that he repeatedly raped and sexually assaulted her at the Kuravilangad convent between 2014 and 2016, a charge denied by him.
According to police, no visible injury marks were found on the body of the priest.
Sister Lucy Kalappura, one of the nuns who protested against rape-accused Bishop Franco Mulakkal, in her autobiography titled 'Karthaavinte Naamathil' (In the name of the Lord) writes that even church leaders who supported the sisters, the victims of sexual abuse, have now started supporting the accused.
The nuns -- Alphy, Anupama, Josephine and Ancitta -- were served notice by the superior general of the congregation, Regina Kadamthottu, urging them to take up their assigned responsibilities as befitting members of the Missionaries of Jesus congregation.
Franco Mulakkal, accused of raping a nun several times between 2014 and 2016, is currently out on bail.
The clergyman has been shifted to the sub-jail in Pala after completing his medical examination at a government hospital.
The nun alleged that she was subjected to sexual abuse 13 times.
With the controversy over 'love and narcotic jihad' remark by Pala Bishop Joseph Kallarangatt refusing to die down, the Congress and the Bharatiya Janata Party on Monday engaged in a fresh round of verbal sparring.
His lawyers moved the application, submitting that the clergyman was arrested after a three-day-long interrogation by the probe team.
Police had said the nun was subjected to rape and unnatural sex by the accused at the guest house of St Francis Mission Home 13 times between 2014 and 2016.
The Bishop will have to surrender his passport and his entry to Kerala will be restricted.
In a press release, the congregation accused the victim, her five fellow nuns and four others of conspiring against the bishop.
The 54-year old Mulakkal was arrested by Kerala police after intense interrogation in Kochi over the last three days.
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