The matter came up for hearing before a three-judge bench of Justices Arun Mishra, Vineet Sharan and S. Ravindra Bhat.
However, Justice Bhat recused himself from hearing the matter, after which the court referred the case to another bench.
This the third time a judge has recused himself from hearing the case. On October 1, a three-judge bench of Justices N.V. Ramana, B.R. Gavai and R. Subhash Reddy had recused itself from hearing Navlakha's plea.
Before that Chief Justice Ranjan Gogoi had removed himself from the case.
The Bombay High Court had on September 13 rejected Navlakha's plea seeking to quash the FIR filed against him early last year by the Pune Police for his alleged Maoist links and involvement in the Bhima-Koregaon and Elgar Parishad cases.
Soon after the Bombay High Court rejected his plea, the Maharashtra government filed a caveat in the Supreme Court anticipating Navlakha's appeal against the High Court's order. A caveat means the court cannot pass an order without hearing the other side.
Navlakha and nine other human rights and civil liberties activists were arrested by the Pune police from different parts of India, for their role in Pune's December 31, 2017 Elgar Parishad gathering that served as a trigger for the caste riots in Bhima-Koregaon the next day, on January 1, 2018.
Among other things, they are accused of having alleged links with the banned CPI-Maoist, a conspiracy to assassinate Prime Minister Narendra Modi and to overthrow the elected government.
( With inputs from IANS )