Deputy Superintendent of Police Lokayukta C K Shashidhar filed the FIR under various sections of IPC and the Forest Act against Bopaiah, who represents Virajapet in the Assembly, and three officials.
Several former BJP ministers and MLAs, including former chief minister B S Yeddyurappa, are facing Lokayukta police probe based on private complaints.
The case was filed following a directive by District and Sessions Judge Ashok Nijagannanavar, also the judge of the Special Court for prevention of corruption cases, on the complaint filed by Congress Zilla Parishad member Saritha Poonacha on December 2.
Others named in the FIR are Zilla Panchayat Member S N Raja Rao, Nirmiti Centre Project Director Yoga Narasimha, ZP CEO Krishnappa.
The complaint alleged "misuse of funds" to the tune of Rs 40 lakh out of Rs 1.2 crore sanctioned for construction of a lake in a rehabilitation centre for tribals in Reshme Hadlu in Titimathi, 60 km from here, during 2006-07 when Bhopaiah was an MLA.