Mr Naik pointed out that the judge who took over the case, subsequently, within 29 days of the death of judge Loya, discharged Mr Shah from the case, accepting an application filed by him.
As advocate Varinder Kumar Sharma initiated arguments briefly on behalf of the petitioner, Congress sympathiser and relative of Robert Vadra, Tehseen Poonawalla, the court said, "This matter requires bi-party hearing rather than exparte".
CBI judge Loya died under mysterious circumstances in 2014 and during the time of his death, he was hearing Sohrabuddin Shiekh fake encounter case in which BJP President, Amit Shah is an accused.
The court rejected a plea by senior advocates Dushyant Dave and Indira Jaising not to consider these two petitions.
The sister of the judge had later said that the then Bombay High Court Chief Justice Mohit Shah allegedly made an offer of Rs 100 crore to her brother fabourable judgement.
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The Bench, before adjourning the matter, asked the counsel appearing for the state of Maharashtra to seek instructions.
Justice Loya's death in mysterious circumstances had become one of the most debated issues of the previous year, and it looks like the case has bled into the year as well.
Earlier, as many as 470 members of Punjab and Haryana High Court Bar Association had written to the Chief Justice of India asking for an independent inquiry of Judge BH Loya.
A total of 23 accused, including police personnel, are now facing trial for their involvement in the alleged fake encounter of Sohrabuddin Shaikh, his wife Kausar Bi and their associate Tulsidas Prajapati in Gujarat in November 2005. The case was later transferred to the CBI and the trial was shifted to Mumbai.
Loya had gone to Nagpur to attend the wedding of a colleague's daughter on November 30, 2014, when he apparently fell ill suddenly and died of a heart attack.