A case under the Prevention of Corruption Act and the IPC was registered at the Bund Garden police station, where a Pune-based activist and builder, Hemant Gavande, had filed a complaint on May 30 last year, an official said.
Superintendent of Police (ACB) Shirish Sardeshpande confirmed that the case was registered against Khadse, his wife Mandakini, son-in-law Girish Chaudhary and the original owner of the land Abbas Ukani.
However, after Pune police did not register an FIR, Gavande had moved the Bombay High Court and since then the bench was hearing his petition.
"The complaint application filed by Gavande on May 30, 2016 at Bund Garden police station will be treated as the main complaint and now since the FIR has been registered, the ACB will investigate that original complaint. Gavande is the complainant in today's FIR," Sardeshpande said.
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Expressing happiness over the development, Gavande said, "I am happy and I feel that justice is still alive. As the case has been registered now, the ACB should prove the intention behind the purchase of such a land, which is acquired and possessed by MIDC."
On March 8, the Maharashtra government had told the court that ACB would probe the case against Khadse and would register an FIR. The HC had said that the investigation should be carried out "expeditiously and independently".
Khadse had quit the Devendra Fadnavis ministry in June last year in the wake of a string of allegations, including irregularities in the Pune MIDC land deal.
The state government had earlier set up a judicial commission, headed by retired Justice Dinkar Zoting, to probe the allegations against Khadse in this matter.