Mulakkal, who is the bishop of the northern Indian city of Jalandhar, has denied the accusations.
On Thursday, the Apostolic Nunciature (Pope's Ambassador) to India accepted the request of the rape accused Bishop to relieve him of his religious duties temporarily.
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Mulakkal has called the whole scandal a conspiracy by those against the Church, and has won backing from his congregation at the Missionaries of Jesus Church. The Kerala Police registered a case against Missionaries of Jesus after the nun's brother filed a complaint. The protests gained momentum after members of the civil society, actors and social activists joined the protests. "The Kerala high court should not give him bail on September 25", said Hamid Masih, the movement's president. "He has been arrested under the pressure of the protest led by nuns. It's been 74 days since she gave a complaint, but other than the police questioning the victim, we don't see any other progress".
The Catholic Bishops' Conference of India (CBCI) had said on Thursday that Pope Francis had temporarily relieved Mulakkal of his pastoral responsibilities, a decision welcomed by the protesting nuns who termed the development as the "first victory" in their fight against the former bishop. The statement has also said that the allegations against the bishop are completely baseless. "If the allegations are proved right, we are ready to boycott him".
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Three teams are probing Fr Mulakkal, who has been accused of raping a nun 13 times over a period of two years at different places.
The bishop has been charged under four counts including rape, illegal confinement and criminal intimidation.
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The nun alleged that Mulakkal raped her at a guesthouse in May 2014 and later attacked her on several more occasions.