On 15 March 1983, Mukharji was appointed as a judge of the Supreme Court of India, and he became Chief Justice of India on 18 December 1989. In March 1989, Mukharji became involved with the Bhopal gas incident when he was appointed to head the Supreme Court's panel to examine the vadility of the "Bhopal Gas Leak Act" ("Bhopal Settlement Act"). He issued his initial opinion just five days after becoming Chief Justice, but did not live to see the court's final disposition of the matter. It was also during his term in the summer of 1990 that corruption charges surfaced against judges on the Bombay High Court, which caused a "crisis of credibility" in the judiciary for the whole country. Charges of corruption, nepotism, casteism and politicisation of appointments for most of the high courts began to make the news. Mukharji worked to keep the judiciary independent and worked to solve the problems. Justice Mukharji has received criticism for his handling of the V. Ramaswami case, where his appointment of a committee did not result in corrective action, although Parliament was almost unable to resolve that case. Regarding the conduct of judges, Mukharji said: "The Judges either of the Supreme Court or the High Courts and the Chief Justice are subject to the rule of law like any other citizen of this country and must abide by the norms and regulations prescribed in as much as these and to the extent are applicable to them. I always thought this was clear and need no reiteration. We must therefore, ensure that there is no conduct of the Judges which affects the faith of the people that Judges do not live according to law."