The bank accounts, which the society claimed to have opened to meet litigation cost by the members, were frozen by CBI during the probe into the 2010 Adarsh scam.
A bench of Justices J Chelameswar and Sanjay Kishan Kaul said that bank accounts will be defreezed and the society will deposit security of immovable assets to the satisfaction of special court at Mumbai.
Senior advocate Meenakshi Arora said that the amount lying in these bank accounts had nothing to do with the investigation as it was collected by the members of society to meet litigation cost.
The arguments were opposed by the counsel appearing for the CBI, who said that amount need not be allowed to be withdrawn as it is very important to establish the money trail.
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He said that Adarsh society is a "building of shame" and several benami properties were found.
"These accounts had benami transactions and if money is allowed to be withdrawn then it will be very difficult for the agency to prove the cash trail," he said.
The Adarsh scam had kicked up a political storm leading to the resignation of the then Congress chief minister of Maharashtra, Ashok Chavan. The 31-storey Adarsh apartments was built at Colaba in posh South Mumbai locality for 1999 Kargil war heroes and war widows.
The Bombay High Court had earlier ordered demolition of the apartments and sought initiation of criminal proceedings against politicians and bureaucrats for alleged misuse of powers, holding that the tower was illegally constructed.
It had also asked the Centre and Maharashtra government to consider initiating civil and criminal proceedings against bureaucrats, ministers and politicians for misuse and abuse of power to get plots under the scheme, originally meant for Kargil war heroes and war widows.
The top court in July last year had said that the Adarsh apartments would not be demolished for the time being and asked the Centre to secure it after taking its possession from the housing society.
In 2011, the Maharashtra government had set up a two- member judicial commission headed by Justice J A Patil to inquire into the Adarsh scam.
Later, the CBI, the Income Tax Department and Enforcement Directorate (ED) also investigated the scam.