A former Supreme Court judge and eminent criminal law expert, he was appointed as the chairperson of Justice Mukherjee Commission of Inquiry (JMCI) in 1999. His name was recommended by the then Chief Justice of India. Mukherjee’s inquiry was lauded by all those who had stakes in the matter in any way. He conducted his inquiry strictly in accordance with the Commissions of Inquiry Act and the terms and reference assigned by the Central Government. At a press conference in Kolkata on 26 May 2006, no less than 43 members of Netaji Subhas Chandra Bose’s family praised Justice Mukherjee’s efforts. Their joint statement said:
We, the overwhelming majority in the Bose family, deeply appreciate the arduous efforts that Mr Justice MK Mukherjee and his team in the Commission have made for seven years…we admired the way Mr Justice Mukherjee conducted himself in public hearing. Approaching delicate issues in an objective manner, he rigorously sought evidence for any statement made before him. Nobody can question either his competence or his integrity.