Justice U U Lalit who was part of the bench headed by Chief Justice of India T S Thakur recused himself without citing any reason.
The matter was posted for further on February 26, before a bench in which Justice U U Lalit is not a member.
The plea filed by activist Bennet Castelino sought CBI probe into the mysterious disappearance of key prosecution witness Rahul Sachan since November 25 last year. Sachan was also stabbed in Jodhpur court on February 13, 2015 where he was summoned as prosecution witness in the case.
The petition further said that Rajasthan, Uttar Pradesh and Gujarat governments were conducting parallel probes into Sachan's disappearance but till date he has not been traced.
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"He was in constant touch with the Petitioner and had told the Petitioner that in case there is no contact with him, the Petitioner must immediately alert the police authorities and make an application to the Supreme Court for a probe as he feared for his life," it said.
The petition further said, "It is not the case of the Petitioner that the Accused are involved in the deaths and threats of Prosecution Witnesses but the Petitioner seeks that all witnesses in these cases be protected by the CISF (Central Industrial Security Force) and all cases related to the deaths and threats to witnesses be investigated by the CBI and, if need be, under the monitoring of this Court.