He was escorted by a security team.
The Pope took the decision in response to Mulakkal's September 16 letter offering to "step aside temporarily" as the Bishop of the Jalandhar diocese, Kerala Catholic Bishops Council spokesman Fr Varghese Vallikkattu told PTI.
In June, a nun had complained that Mulakkal had raped her 13 times at the mission house in Kottayam district, over a period of two years from May 5, 2014. The bishop has swiftly denied all the charges which were filed against him and reportedly said that it was a "conspiracy".
An Indian bishop accused by a nun of raping her was arrested Friday, in a high-profile abuse case that had triggered angry protests by clergy over police inaction, Press Trust of India reported.
Kottayam Superintendent of Police Hari Sankar has said the Special Investigation Team (SIT) probing the case has chose to complete the interrogation on Friday.More news: Klopp laughs off Salah's lack of goals
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Pope Francis relieved Mulakkal from duty on Thursday and appointed another bishop in his stead. REUTERS/Sivaram V Bishop Franco Mulakkal (2nd R), accused of raping a nun, is pictured outside a crime branch office on the outskirts of Kochi in the southern state of Kerala, India, September 19, 2018.
A team of Kerala Police headed by DSP K Subhash had travelled to Jalandhar to question the Bishop regarding the case.
Police in India are now investigating the charges of rape, illegal confinement, unnatural sex and intimidation. She said she had to approach police because church authorities did not act on her complaints. One of the nuns, while slamming the police's inaction in nabbing the accused said, "The police have repeatedly taken the statement of the victim nun, but they have taken Franco Mulakkal's statement only once".
The arrest comes at a time when the state's Christian community is reeling from a string of cases - including the arrests of five priests last month on allegations of sexual assault.