MUMBAI, India – Cardinal Oswald Gracias, the president of the Catholic Bishops’ Conference of India, says the bishops of the country are “deeply pained” over the case of a bishop accused of rape, and “the constant attacks by the media on the Church implying that it was trying to cover up this case.”

Bishop Franco Mulakkal has been accused of raping a nun several times between 2014-2016. After a months-long investigation, police arrested him on Sep. 21.

Gracias, the Archbishop of Bombay, said on Sunday Church authorities “have studied and continue to examine this serious and complex matter,” but added that any accusation of a Church cover-up “does not correspond to the truth.”

“Since the civil authorities were making their investigations, the Church did not make any statement. We realize that such matters require time and discernment. We reiterate that we have full confidence in the judicial system of our country,” Gracias said.

Mulakkal is the Bishop of Jalandhar, in the northeastern state of Punjab. The nun making the accusation is a member of the Punjab-based Missionaries of Jesus Congregation.

The rapes are alleged to have taken place in the order’s convent in Kuravilangad in the southern state of Kerala.

The police in Kerala are conducting the investigation, and the Kerala High Court will hold a bail hearing for Mulakkal on Oct. 3.

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.

The bishop has vehemently denied the charges, and says the nun is retaliating against him for investigating a complaint that she had an affair with a married man. The religious congregation has steadfastly defended Mulakkal against the accusations made by the nun, who once held a leadership position in the order. The order has also criticized its own members in the Kuravilangad convent for supporting the nun making the accusations.

The case has been widely covered by the press in India, and the bishops have been criticized for not being proactive in the case. Mulakkal has also been accused by supporters of the nun making the rape accusation of using his influence with political leaders in Kerala to try and block the investigation.

In his message, Gracias invited “all people of good will” to pray for everyone involved – “that their sufferings might be alleviated, the spiritual wounds healed, the truth recognized and that justice be done.”

On Oct. 1, three bishops visited Mulakkal in his jail cell in the city of Pala, Kerala. Bishop Mathew Arackal of the Syro-Malabar Catholic Eparchy of Kanjirappally, his auxiliary, Bishop Jose Pulikkal, and Bishop Samuel Irenios Kattukallil, Coadjutor Bishop of the Syro-Malankara Diocese of Pathanamthitta are eastern rite Catholic bishops based in Kerala.