"Not before me", said Justice Revati Mohite-Dhere when the petition came up before her, without assigning any reason for not hearing it.
The matter would now be heard by another bench, said High Court sources.
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A special CBI court had earlier turned down the investigating agency's plea to drop Chavan's name from the First Information Report (FIR) in the case.
CBI had filed the application after Maharashtra Governor K Sankaranayanan refused sanction to prosecute Chavan on the ground of inadequate evidence.
Chavan had to step down as the Chief Minister after the scam came to light in 2010.
The CBI had charge-sheeted Chavan in 2012, accusing him of granting Adarsh housing society various concessions in return for flats for his relatives.
Chavan was alleged to have approved additional floor space index for the highrise in upscale Colaba in south Mumbai and, as Revenue Minister, allowed civilians to be included as members of the housing society meant for Kargil war widows and defence personnel.