Justice J.S. Khehar led the five-judge Constitution Bench in Supreme Court Advocates on Record Association v. Union of India . By enabling the collegium system to continue, Justice J. S. Khehar, quashed the NJAC Act and also declared 99th Amendment to the Constitution unconstitutional. The majority concluded this judgment: While adjudicating upon the merits of the submissions advanced at the hands of the learned counsel for the rival parties, I have arrived at the conclusion, that clauses and of Article 124A do not provide an adequate representation, to the judicial component in the NJAC, clauses and of Article 124A are insufficient to preserve the primacy of the judiciary, in the matter of selection and appointment of Judges, to the higher judiciary. The same are accordingly, violative of the principle of "independence of the judiciary." Justice Khehar further explained: that clause of Article 124 A is ultra-vires the provisions of the Constitution, because of the inclusion of the Union Minister in charge of Law and Justice as an ex officio Member of the NJAC. Clause of Article 124A, in my view, impinges upon the principles of "independence of the judiciary", as well as, "separation of powers". It has also been concluded by me, that clause of Article 124A which provides for the inclusion of two "eminent persons" as Members of the NJAC is ultra vires the provisions of the Constitution, for a variety of reasons. The same has also been held as violative of the "basic structure" of the Constitution. But fascinatingly, Justice Khehar admitted that all is not well even with the collegium system and this is the time to improve it. However, the Supreme Court invited the government to help the judiciary to improve and better the existing collegium system.
A three judges Bench of the Supreme Court headed by Justice J S Khehar upheld cancellation of admission of more than 300 candidates
Justice J. S. Khehar also headed a historic five judge Constitution bench in Nabam Rebia & Bamand Felix v. Bamang Felix Deputy Speaker & Others, that reinstated the Congress-led Arunachal Pradesh Government and held all the actions of the Governor violative of the Constitution. Alluding S. R. Bommai v. Union of India Justice Khehar avowed that it had: "all the powers to put the clock back". The Supreme Court Bench headed by Justice J S Khehar imposed an exemplary cost of Rs. 25 lakh on NGO Suraz India Trust for filing 64 frivolous cases in various high courts and also in the apex court and wasting the judicial time.. Justice J S Khehar in State of Punjab vs. Jagjit Singh gave a significant verdict holding that the principal of 'equal pay for equal work' has to be made applicable to those engaged as daily wagers, casual and contractual employees who perform the same duties as the regulars. Justice J S Khehar was also a part of the bench which sent Sahara Chief Subrata Roy to jail while hearing the matter relating to the refund of money invested by people in his two companies. As an aftermath of Supreme Court's landmark decision in the 2G spectrum case, Govt of India filed a Presidential reference before the Supreme Court. Justice Khehar gave a separate concurring opinion in which he warned that the government should not be under erroneous impression that it is not necessary to allocate natural resources through auction. Heading a three-judge bench of Punjab and Haryana High Court Justice Khehar decided a case involving definition of a Sikh. He held that religion must be perceived as it is, and not as another would like it to be. Justice Khehar was one of the judges on multi-faith bench that heard the controversial Triple Talaq case in 2017. Though Khehar upheld the practice of validity of Triple Talaq, it was barred by the bench by 3:2 majority and asked the Central government to bring legislation in six months to govern marriage and divorce in the Muslim community. The court said till the government formulates a law regarding triple talaq, there would be an injunction on husbands pronouncing triple talaq on their wives.
Controversy
In 2017, the Committee on Judicial Accountability published the suicide note written by former Arunachal Pradesh Chief Minister, Kalikho Pul. In the note, Pul claimed that Khehar had demanded ₹49 crore and ₹31 crore in bribes from Pul for delivering a favourable verdict. The Committee on Judicial Accountability has demanded a probe in the matter. Taking into account the serious allegations against various constitutional functionaries, Justice Khehar directed that the whole matter requires a serious judicial deliberation. Pursuant to this order, the matter was listed before a division bench. However, Ms. Dangwimsai Pul, wife of former Arunachal Pradesh CM Kalikho Pul, decided to withdraw her letter to Khehar on the pretext that "the letter will lead to closure of other remedies". Accordingly, the petition was dismissed as withdrawn. . Later, the Delhi High Court on 22 May 2017 rejected the plea filed by National Lawyers Campaign for Judicial Transparency and Reforms for lodging an FIR on the allegations made in a purported suicide note of former Arunachal Pradesh Chief Minister Kalikho Pul. The High Court held that the petition "did not vouch for the authenticity" of the alleged suicide note and imposed a cost of Rs 25,000 on each of them, totalling Rs 2.75 lakh, saying the petitioners were "busy-bodies" making "wild allegations". In yet another controversy involving CJI Khehar, High Court Judge C.S. Karnan ordered a psychological evaluation of Khehar. On 8 May 2017 C S Karnan ordered a punishment of 5 years of rigorous imprisonment and a fine worth Rs. 1 lakh on Jagdish Khehar.
