The state government, on Friday, had announced Satyanarayana Rao, Additional DGP, Crimes & Technical Services as the replacement of Gaonkar.
"Some people ultimately got bail and they came out but inquiry against them and their family and former colleagues is continuing," said Santosh Hegde.
The Chief secretary objected Mr Rao's appointment and questioned the "sudden transfer without there being a Lokayukta, without his opinion," as reported by newspapers.
"All this leads to one and only conclusion that this was done for collateral purpose...to sabotage the investigation. An attempt is being made definitely with an objective to defeat the investigation that's being carried out," Hegde alleged.