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President Pranab Mukherjee rejected Yakub Memon's mercy petition sent to him on Wednesday.
Activists and Memon's lawyers told the Supreme Court in a late-night appeal that after a mercy plea is rejected, the death row prisoner can't be hanged for 14 days, according to rules.
However, the three Supreme Court judges who heard the case accepted the government's argument that Memon had "ample opportunity" to challenge his sentencing.
The court accepted the government's argument that a mercy plea filed on Memon's behalf by his brother, which was rejected by the President last year, could not be overlooked.
The Supreme Court on Wednesday had refused to stop Memon's hanging, rejecting his claim that the top court had not followed correct processes in upholding his death sentence earlier this week.
The same three judges who ruled against him during the day heard the emergency petition in the middle of the night.
Memon was convicted for helping finance the serial blasts in Mumbai in 1993 in which 257 people were killed.
His brother, Tiger, and Dawood Ibrahim, who masterminded the blasts, remain missing.
Those who support Memon's claim say that he provided crucial information to investigators in fixing accountability for the blasts. Two of his brothers have been given the life sentence.
Memon left the country just before the blasts. He returned a year later amid conflicting reports on whether he had been arrested or had surrendered. Investigators deny he was offered a secret plea bargain.
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