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The 54-year-old clergyman would be produced in a magistrate court in Pala later in the day.
He had complained of pain in his chest while being taken to Kottayam Police club from the Crime Branch office in Thrippunithura in Ernakulam district Friday night, they said.
He was under observation in the cardiology section of the Medical College Hospital for over 6 hours after his blood pressure shot up, they said.
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In her complaint to the Kottayam Police in June, the nun had alleged that Bishop Mulakkal raped her at a guest house in Kuravilangad in May 2014 and later sexually exploited her on several occasions.
She said she had to approach the police as the church authorities did not act on her repeated complaints against the clergyman.
However, the bishop has denied the charges.