Refusing to comment on the matter, Ms Roopa said, "The government has its own right to transfer officials". "I came to join my new department. Let me join my new department," she added.
The BJP, which held protests outside the state assembly in Bengaluru, has accused the Congress government led by Siddaramaiah of victimizing the officer.
"Siddramaiah is sending a clear message to all the honest officers that they will not be tolerated and they will be punished by transfer if they approach any whistle blowing activity," said state BJP leader S Prakash.
The Congress has dismissed the allegations.
Mr Rao held a press conference and said the allegations were "baseless" - a comment that was immediately challenged by Ms Roopa. Within days, she was transferred and Mr Rao, who is to retire by the end of this month, was asked to go on leave.
The government said both officers had violated service rules by speaking to the media. The transfer of Ms Roopa and the removal of Mr Rao was necessary to "maintain the sanctity of the inquiry," the government said at a press conference.