In late 1995, Bihar was in a financial crunch. The then charismatic yet 'native' leader Lalu Prasad Yadav was the Chief Minister of undivided Bihar, where the then finance commissioner VS Dubey stumbled upon the financial irregularities of massive scale.[6] In December 1995, Dubey was, as part of his job, reviewing the performance of various departments. He found that money was withdrawn in excess of the allocation by some of the department.[7][8] Khare, who was then District Magistrate at Chaibasa, noted that the district animal husbandry department had withdrawn Rs 10 crore and Rs 9 crore twice without giving any details. Even when questioned, there was no response from the animal husbandry department. Finally, in January 1996,Khare visited the office to investigate, and found it looking as if "someone had tried to destroy files in a hurry".[8] Many bogus bills were for amounts just under Rs. 10 lakhs (when there are more stringent authorization norms). It seemed that such payments had been going on for years. The next day, simultaneous raids conducted at Ranchi and elsewhere found similar practices.[9] This was the first evidence of the scam, which gathered momentum after regional CBI director U. N. Biswas defied political pressures to pursue the case up to the chief minister level. Those convicted include the preceding DM of Chaibasa, IAS officer Sajal Chakraborty.[10]
He has served as Secretary in the Ministry of Information and Broadcasting.[14][15] On 14 December 2019, he assumed charge as Secretary, Ministry of Education (Department of Higher Education) with additional charge of School Education - in background of ongoing negotiations with JNU students regarding fee hike and campus lockdown and served there till 30 September 2021.[16] Thereafter, he was appointed advisor to Prime Minister of India on 12 October 2021.[17]