The church body also released a photograph of the Kerala nun sitting next to the rape accused Bishop.
It also released a statement saying that the picture is just for the evidence and the Missionaries of Jesus would not be responsible if the picture becomes public, reported News Minute. Indian laws prohibit revealing the identity of rape and sexual assault victims.
“The Missionaries of Jesus has understood that the allegations about the Bishop repeatedly raping the nun multiple times between 2014 and 2016 is false and is part of a conspiracy," the statement said.
"In the month of May in 2015, the sister had invited the Bishop for a function and even after that, it has been found that the sister has taken part in a lot of functions with the Bishop. Any woman, who was raped by a man, would never attend functions or travel with that man. This is a truth that cannot be denied," it added.
The congregation claimed that the May 23, 2015 photograph was taken when the nun was attending a private function along with Bishop Franco Mulakkal. They claimed that the nun had attended several such functions with Mulakkal.
The nun has never appeared in public or in front of media after filing the complaint.
In a press release, the congregation accused the victim, her five fellow nuns and four others of conspiring against the bishop.
It alleged that the nuns had "violated the discipline of the congregation" several times and even refused to renew their vows-- a very important step in the life of a nun in a convent.
Framing charges against the nuns, the enquiry commission said the congregation was convinced that they were under the influence of "atheists" and their thoughts.
It claimed that the visitors' register, a key evidence for establishing Mulakkal's presence in the convent in Kuravilangad where the victim nun lived, was handled by a nun very close to her and they might have tampered with it.
It also accused the victim and her fellow nuns of forcibly shifting to their room the control system of the CCTV cameras from that of Mother Superior.
A nun from Kerala has accused that she was raped by Jalandhar diocese Bishop Franco Mulakkal on several occasions between 2014 and 2016.
The nun has even appealed to the Vatican seeking justice.
In a seven-page letter addressed to the Apostolic Nunciature- the representative of the Holy See in India- the victim has described the ordeal she allegedly went through at the hands of the Bishop.
The victim also marked the plea to 21 other high ranking authorities of the Roman Catholic Church in India.
The nuns in Kochi, have been protesting from past four days, against the accused Bishop, demanding action against him.
(With additional inputs from PTI)