He was escorted by a security team. On September 16, Mulakkal had written a letter to Pope Francis and sought permission to temporarily step down from his responsibilities at the Jalandhar Diocese.
There was no immediate comment from Bishop Franco Mulakkal or his lawyers - though he has denied the charges in interviews in the past.
On Wednesday, activists of All India Youth Federation, the youth wing of CPI, waved black flags as the bishop came out of the police station after questioning.
Kottayam Superintendent of Police Hari Sankar said that the Special Investigation Team (SIT) which is probing the case made a decision to complete the interrogation on Friday.
The bishop was taken for a medical examination after his arrest. While the police registered a case in Kottayam on June 28, the probe against him dragged on for almost three months.
Mulakkal, 54, was ordained as a priest in 1990 in the northern Indian Punjab state and was elevated as the bishop of the Diocese of Jalandhar five years ago. Franco Mulakkal had last week handed over administrative responsibility of the Jalandhar diocese to a junior priest in his absence ahead of his Kerala visit. In a letter, the rape-accused Bishop stated that he needed more time to travel to Kerala in order to fight the case. "It is the first victory in our struggle against the Bishop". When the church failed to take action on this matter, the nun approached the Kerala police.
According to The Indian Express, SP Hari Sankar has said that there is a lack of scientific evidence which could substantiate the rape charges and the delay in informing the police is an impediment.