He expressed the fear that if Chishty is not released forthwith, he may die in the jail by the time his appeal is decided by the Rajasthan High Court.
In an e-mail sent to the Prime Minister through Member of Parliament Rajiv Shukla, Justice Katju said Singh should grant pardon to Chishty under Article 72 which empowers the President to sanction pardon or remission for convicts.
Justice Katju said he was writing the letter through Shukla as he did not have the Prime Minister`s person e-mail ID.
In 2010, Chishty was awarded life sentence under 302 IPC in a murder case by a sessions court in Rajasthan after an 18-year trial. He had filed an appeal in the high court but his bail plea had been rejected.
During the trial period, the sessions court while granting him bail had ordered Chishty not to leave Ajmer. He was re-arrested after his conviction.
In his letter, Justice Katju said, "I am making this appeal to you not as a Supreme Court judge, but as a human being, requesting for release of Dr Khalil Chishty, a Pakistani national, who is old and infirm and (is) in Ajmer jail, on humanitarian grounds under Article 72 of the Constitution."
Chishty, who was an eminent Professor of Virology in Karachi Medical College, holds a PhD from Edinburgh University.
During a visit to Ajmer in 1992 to meet his ailing mother, there was a dispute between his family in Ajmer and certain others in which a person was killed following which Chishty was also arrested.
Referring to Chishty`s appeal in the high court, Justice Katju said, "One does not know when the appeal will be heard, and in the meantime Dr Chishty may die in jail since he is so old that he has to be physically carried.
"He is also a heart patient and has (suffered) a hip fracture. It will be a disgrace for our country if he dies in jail."
The apex court judge, however, cautioned that he was not commenting anything on the merits of the case as it is a judicial proceeding.
"However, apart from the judicial proceeding there is executive power in the President and the Governor to grant pardon," the judge said.
According to Justice Katju, eminent film producer/director Mahesh Bhat and others have already appealed to the President under Article 72 of the Constitution, as well as to the Governor of Rajasthan under Article 161 to grant a pardon, so that he may spend the last days of his life in his home in Karachi.
"I join them in this appeal. The relevant papers are with Home Minister P Chidambaram," he said.
He recalled the Supreme Court ruling in the Nanavati vs State case wherein it was held that pardon can be granted even when a case is pending.
"Please, therefore, do the needful in this connection.
Time is the essence of the matter since Dr Chishty has not many years to live. If you need any further details please give an audience to Mahesh Bhat (whose email address has been copied) and others who signed the petition for pardon.
"Needless to mention, if a pardon is granted it will enhance the prestige of India," the judge said.
Quoting from Shakespeare`s `The Merchant of Venice`, the judge said, "The quality of mercy is not strained. It droppeth as the gentle rain from heaven upon the place beneath."
Justice Katju recalled the pardon granted recently to an Indian prisoner (Gopal Dass) by the Pakistan President after the Supreme Court here made an appeal to that country for his release.