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Investigations into the case remain suspended, however. Justices Ashok Bhushan, RS Reddy and MR Shah did not scrap the High Court's ban on a probe into the FIR or First Information Report filed by the Andhra government. The Supreme Court will hear the case next in January-end.
The Supreme Court has sought responses from Andhra Pradesh's top police officer and the state's former advocate general, who had gone to the High Court requesting it to block media reports against him.
The FIR alleges that chunks of land were bought in Amaravati by a group of people who knew it would be declared the new state capital even before the formal announcement in 2015 by the Chandrababu Naidu government of the time. There was mass land pool sharing and the buyers benefited as land prices soared, according to the complaint.
Former Advocate General Dammalapati Srinivas and the daughters of a Supreme Court judge are named in the FIR.
Dammalapati Srinivas, who served as Advocate General for the Chandrababu Naidu government, is accused of using his influence to extract information about the capital plan and then buying premium land in Amaravati using proxies.
The FIR alleged that Mr Srinivas had "entered into a criminal conspiracy" with buyers including the Supreme Court judge's daughters, who are also named in the case.
The Jagan Mohan Reddy government had set up a 10-member Special Investigation Team in February for a comprehensive investigation into the alleged irregularities, particularly the land deals in the Amaravati Capital Region, during the previous regime.
Mr Srinivas's lawyers Mukul Rohatgi and Harish Salve told the Supreme Court that the state government deliberately leaked details of the case to the media to "malign his reputation".
Senior Advocate Rajeev Dhavan, appearing for Andhra Pradesh, said the investigation being put on hold by the High Court was "unwarranted" as the petition before it was for anticipatory bail and to stop media reporting on the case.
Mr Dhavan also referred to documents related to the FIR and said an investigation was needed into why farmers sold their land in Amaravati between June and December 2014.