Sandip Ghosh, who resigned as principal of the British colonial-era college days after the incident became public, was arrested on Monday on charges of financial irregularities, the Central Bureau of Investigation (CBI) said.
The CBI said it also arrested two vendors of hospital supplies and a close aide of Ghosh in connection with the case.
Reuters was not able to immediately reach Ghosh or his lawyer.
The rape and murder case triggered widespread protests by doctors demanding greater safety for women at the workplace and justice for the 31-year-old doctor, whose body was found over three weeks ago.
Although tougher laws were introduced after the 2012 gruesome gang-rape and murder of a 23-year-old student on a moving bus in New Delhi, activists say the incident in Kolkata has highlighted how women in India continue to suffer from sexual violence.
A police volunteer, designated to help police personnel and their families with hospital admissions when needed, was arrested last month and charged with the crime.
