The prosecutor had recently stirred a controversy by alleging that an officer of NIA had told her to "go soft" on the accused, a charge denied by the anti-terror agency.
"I represented certain accused in the matter," Justice U U Lalit said while recusing himself from hearing the case.
The bench, headed by Justice FMI Kalifulla, then said that "let the matter be listed before the Chief Justice of India who, in turn, will allocate it to another bench".
Senior Advocate Indira Jaising, appearing for Harsh Mander who had filed the PIL, said that she had no objection if the present bench decides to hear the matter. The court, however, declined the plea.
The PIL has accused the NDA government of trying to interfere with the functioning of the prosecutor in the case by exerting "pressure" on the prosecutor to "go soft" on the accused. It alleged that the executive was attempting to influence the judicial system.
It alleged that National Investiation Agency (NIA) officials had pressured erstwhile Special Public Prosecutor in case, Rohini Salian, "presumably" under instructions from their "political masters".

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