The departments have to submit these files to the Justice J A Patil Commission appointed by the court.
The Housing Department was given eight weeks while the Urban Development Department was allotted five weeks by a bench headed by Justice Abhay Oka to hand over the files pertaining to alleged double or multiple allotment of flats from the CM's discretionary quota.
The HC had last week admonished the government for delay in handing over the files after the Secretary of the Commission N N Kumbhar filed a written complaint.
The Commission secretary complained that since December 1, the housing department had given only about 500 files out of the total 1,300, while UDD had handed over only 314 out of the 12,000 files, despite reminders.
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The PIL, filed by activist Ketan Tirodkar, alleged that many people got more than one flat under the scheme by making false declarations. Further, most beneficiaries of the scheme were politicians or those who were close to the politicians, it says.
The court had also ordered that the government must ensure that those who got multiple flats handed the possession back.
The government has filed FIRs against 27 persons for getting flats allegedly fraudulently. The allotment under the CM's quota has been stopped following the court's order.
Under the scheme, the flats were supposed to be given to freedom fighters, artists, sports-persons, etc.