Guru was executed and buried at Delhi's Tihar Jail on Saturday morning in a top-secret operation. Two days later, his family received a letter from the government on Monday which said that Guru's mercy petition had been rejected by the President, and that he was to be hanged.
The Home Minister has said that a letter was sent via speed post to Sopore, Guru's hometown in the Kashmir Valley, on the midnight of February 7. Many have pointed out that even if it had reached the family on time, there would have not been enough time to travel to Delhi to meet him one last time.
Guru spent nearly eight years on death row for his role in the terror attack on Parliament in 2001.
Sources say the Prime Minister spoke to Mr Shinde on Tuesday and asked why the required process was not followed. He also reportedly asked why the Home Ministry relied on a letter to contact his relatives.
Guru's family, human rights activists and many others have attacked the government for its mishandling of his family, and for denying him a last request to meet them.