The Bombay Lawyers' Association (BLA) sent the letter on the issue to the office of Acting Chief Justice V K Tahilramani.
In the letter, the BLA said the recent change in assignments that resulted in transfer of the batch of petitions challenging the discharge of some senior IPS officers in the alleged fake encounter case of Sohrabuddin to a new single-judge bench, sent out a "wrong signal" to the public.
On February 24, the assignments of some of the judges in the high court were changed and the petitions related to the encounter case were transferred from the court of Justice Revati Mohite-Dere to that of Justice N W Sambre.
This, despite the fact that Justice Mohite-Dere had been conducting day-to-day hearings on the petitions and had heard arguments on three of the five petitions, the BLA said.
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"While there is no doubt that the Chief Justice is the master of the roster, this power must be exercised in consonance with conventions, and above all, while keeping in mind the larger public interest," the association has said.
"This (change in assignments) is particularly intriguing considering how Justice Mohite-Dere had consistently reprimanded the CBI for its approach in the case.
"It is necessary to point out that of the 38 accused in the encounter case, 15, including BJP president Amit Shah have been discharged. Out of the 42 witnesses examined so far, 34 have turned hostile," the letter said.
"However, Justice Gavai is the same judge who had given a statement to the press declaring there was nothing suspicious about the death of judge B H Loya," it has said.
The association is yet to receive any response from Justice Tahilramani's office.
Sohrabuddin, a gangster, and his wife Kausar Bi were killed allegedly in a fake encounter by the Gujarat ATS in December 2005. Sohrabuddin's aide Prajapati, who was a witness to the duo's encounter, was killed a year later by the Gujarat and Rajasthan police allegedly in another stage-managed gunfight.
However, questions were raised over the alleged mysterious death of judge Loya and petitions were filed in the Supreme Court seeking an independent probe into the matter.
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