The crucial order called the Chief Justice of India an "institution in himself" and said to "undermine his authority and say he will exercise power arbitrarily is misconceived".
"No doubt the CJI is the master of roster. But why a situation has been created to declare that?" Justice Balakrishnan said. "Everyone knows the institution (the Supreme Court) is in problem. Lawyers say they are all not happy with what's happening in the Supreme Court".
Questions about the allocation of cases have been raised since four seniormost judges of the Supreme Court, in an unprecedented press conference in January, criticised the functioning of the top court.
The rift, which grew in the aftermath of the allocation of a sensitive case on the death of special judge BH Loya, had split the judiciary down the middle. The case had been assigned to Justice Arun Mishra, a judge who is number 10 in the Supreme Court hierarchy.
As late as last week, Justice Jasti Chelameswar, one of the four dissenting judges, said there should be transparency in the allocation of cases, else there will be "suspicion".
Today, the top court said seniority in terms of appointment "has no bearing" on which cases a Judge should hear.
"The Chief Justice of India must act fairly in all matters and treat all judges equally. Let us hope for the best," said Justice Balakrishnan.