Violating a Supreme Court order, the 25-year-old victim in the Raghaveshwara Bharati Swami sexual harassment case was allegedly subjected to a two-finger test at KIMS.
According to a report in The New Indian Express, the incident came to light after the victim suffered an infection.
Earlier this week, the victim had lodged a complaint against the seer, with the Girinagar police in Bengaluru with the help of womenâ€™s group Janawadi Mahila Sangathane (JMS).
The state government later handed over the case to the CID.
Activists have termed the KIMSâ€™ authorities act inhuman and a violation of oneâ€™s right to privacy and have decided to seek a report from the health department.
The woman had said in the complaint that the seer allegedly sexually assaulted her between 2006 and 2012, and told her that she would be destroyed if she told anybody about it.
Raghaveshwara Bharati Swami heads the Ramachandrapura Mutt in Hosanagara, Shivamogga district, which is a Mutt of the Havyaka Brahmin community.
This is the second complaint of rape against the seer. The first was filed in August 2014 by a singer who performed the Ramakatha for the Mutt.