The apex court said it was duty-bound by the seven- judge bench's order in the case and "cannot override it".
"The matter has been heard by a seven-judge bench and order has been passed. The order is binding on us. We in vacation cannot override it. It is nothing we can do," a vacation bench of Justices D Y Chandrachud and S K Kaul said.
However, the bench said, "All equity is subject to law and judicial discipline. You mention the matter before the bench of chief justice."
Nedumpara contended that the bench had all the power to pass an order granting bail and suspension of the six months sentence, as the detailed judgement in the case was yet to be passed by the seven-judge bench.
The submissions did not impress the bench which declined to entertain his plea.
Karnan has the dubious distinction of being the first sitting high court judge to be awarded a jail term by the apex court and also the first to have retired as a fugitive.
A customary farewell by the high court administration to the retiring judge could not be held in the Calcutta High Court as Karnan was not present.
Despite several attempts, Karnan has failed to get any relief from the apex court's vacation benches which has refused to hear his plea seeking a stay of its jail term order.
His lawyers also claimed to have approached President Pranab Mukherjee for exercising his power to stay the apex court's order, but there has been no relief for the ex-judge.
After being sentenced, Karnan had on May 12 moved the apex court for relief, saying neither the high courts nor their judges were "subordinate" to it.
Karnan had said the Contempt of Courts Act was a "cathartic jurisprudence which belonged to the Dark Ages, the era of inquisition and torture, distinct from the classical Roman Law which constitutes the foundation of modern jurisprudence".
He had also sought a stay on all "further proceedings" pursuant to the May 9 order.
Earlier, the apex court had issued a bailable warrant against him to secure his presence in the contempt case.
He had appeared before the apex court on March 31, a first in Indian judicial history, and had asked for restoration of his powers as a precondition for his re- appearance, but the plea was rejected.
He was transferred from the Madras High Court for his repeated allegations and run-ins with its then chief justice and fellow judges.
The high court judge had on February 15, 2016 stayed his transfer order, which was later suspended by the Supreme Court.
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