Police had said the nun was subjected to rape and unnatural sex by the accused at the guest house of St Francis Mission Home 13 times between 2014 and 2016.
The clergyman has been shifted to the sub-jail in Pala after completing his medical examination at a government hospital.
His lawyers moved the application, submitting that the clergyman was arrested after a three-day-long interrogation by the probe team.
They alleged that the police probing the case was trying to sabotage the investigation.
The nuns -- Alphy, Anupama, Josephine and Ancitta -- were served notice by the superior general of the congregation, Regina Kadamthottu, urging them to take up their assigned responsibilities as befitting members of the Missionaries of Jesus congregation.
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