The recommendation, recently sent to President Pranab Mukherjee, was based on the Maharashtra government's decision that the mercy petition be rejected, a senior official said.
Yakub, a chartered accountant and brother of fugitive terror mastermind Tiger Memon, was sentenced to death by a TADA court in 2007 after being found guilty of charges of criminal conspiracy and for arranging finances and managing its disbursement through the co-accused in the Mumbai serial blasts.
Upholding the Mumbai TADA court's verdict, Supreme Court, in March, 2013, had said, "It is not a hyperbole to state that he was one of the driving spirits behind the plan."
Yakub was arrested from Kathmandu airport in 1994. He was later described by the TADA court as being the mastermind who played a key role in the conspiracy, thus "warranting death penalty".
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The multiple blasts had claimed 257 lives and left 713 injured. CBI, which probed the blasts cases, alleged that the conspiracy was hatched by Dawood Ibrahim and other absconding persons, including Yakub's brother Tiger Memon, who is believed to be hiding in Pakistan.
Meanwhile, Home Ministry has decided to convey to Supreme Court that Tamil Nadu government's announcement about freeing all seven convicts in the Rajiv Gandhi assassination case was based on "extraneous considerations".
Immediately after Supreme Court commuted the death sentence of the three convicts in the case on February 18, Tamil Nadu government had informed the state Assembly that a decision had been taken to remit their life sentence, along with that of four other convicts.
Home Ministry had also sent two letters to the Tamil Nadu government detailing all legal and constitutional provisions which say that state governments have no power of remitting life sentences of prisoners as they are convicted under central laws.