In an affidavit, CBI said the governor had refused to grant sanction to prosecute Chavan, but the issue was outside its purview.
The affidavit came in response to a PIL filed by former journalist Ketan Tirodkar, seeking prosecution of Chavan and some others in Adarsh case.
The division bench headed by Justice P V Hardas asked Tirodkar to file a rejoinder by August 8.
The court also sought a report on probe into "benami" (proxy) purchases of flats in the society. In many cases, people, as proxies for prominent political leaders, allegedly bought flats in the multi-story Adarsh society, the PIL alleged.
Chavan is accused of granting illegal concessions to the society in return for two flats for his relatives.
The CBI affidavit, while seeking dismissal of PIL, said that investigation was over and charge sheet was filed against R C Thakur and 12 others on July 4, 2012. Further, supplementary charge sheet was also filed under Benami Transactions (Prohibition) Act against 21 benami flat holders and 24 financers.