MUMBAI, India – Police in India have arrested a bishop accused of raping a nun on 13 different occasions between 2014-2016.

Bishop Franco Mulakkal was taken into custody on Friday in Kochi, in the southern state of Kerala, after three days of interrogation.

The nun making the accusations went to the police on June 29. Mulakkal has vehemently denied the charges, and says the nun is retaliating against him for investigating a complaint she had an affair with a married man.

Mulakkal is the Bishop of Jalandhar, in the northwestern Punjab state, the same state where the nun’s order – the Missionaries of Jesus – is headquartered.

The sexual assaults were alleged to have taken place at the order’s convent in Kuravilangad in Kerala.

Kerala is the state with the highest percentage of Christians in India and provides many of the clergy and religious throughout the country. The Kuravilangad convent had special housing for Kerala-born clergy visiting home, where Mulakkal stayed when visiting the state.

Sources told Mathrubhumi, a local newspaper, that the bishop will be medically examined.

A government minister for the state of Kerala told reporters the “investigation is going in the right direction.”

“The government is with the victim [and] the nuns staging the protest. Certainly, the government will take all necessary steps to identify the culprits and bring the guilty to book,” said E.P Jayarajan, the Minister for Industries and Sport.

On Thursday, Pope Francis accepted Mulakkal’s request to be relieved of his duties during the investigation, naming Bombay Auxiliary Agnelo Rufino Gracias, who will temporarily serve as apostolic administrator of Jalandhar.

“Sexual abuse is a crime and should be dealt with by the law. The arrest is a good thing at the moment for the church to come out clean,” said Father Frederick D’Souza, the former director of Caritas India.

“The approach of the church is to follow the law of the land and cooperate with legal systems and face legal mechanism. The church is law-abiding, and not avoiding,” he told Crux.

On Tuesday, the bishop applied to the Kerala High Court for an anticipatory bail, telling the court the charges against him were a “cooked up story to wreak vengeance.”

The court adjourned the hearing of the application until Sept. 25.