Gopinathan, a 2012 IAS officer from Kerala posted in Dadra and Nagar Haveli as Power and Non-Conventional Energy Secretary, said there was denial of "fundamental rights" to lakhs of people in Jammu and Kashmir for weeks after the state lost its special status earlier this month.
Gopinathan put in his papers on August 21. He had been in the news last year for his role in the flood relief efforts.
"I joined civil service with the hope that I can be the voice of those who have been silenced. But here, I lost my own voice," Gopinathan said after his resignation.
The AGMUT cadre IAS officer, Gopinathan had tweeted on August 20: "I once thought being in civil services meant an opportunity to expand the rights and freedoms of fellow citizens!
"In (Jammu and) Kashmir, fundamental rights of lakhs of people have been suspended for 20 days. And many in India seem to be okay with it. This is happening in India in 2019. Article 370 or its abrogation is not the issue, but denying citizens their right to respond to it is the main issue. They could welcome the move or protest it, that's their right," Gopinathan, instrumental in transforming a loss-making government electricity distribution firm into a profit-making one, told NDTV.
He said the issue "disturbed" him enough to resign.
In his July 31 reply to the Ministry of Home Affairs memo, served on him on July 8, he refuted the charges of insubordination, dereliction of duty and dilatory tactics.
"It is submitted that I have been performing my duties diligently and to the best of my abilities," he wrote, adding he had been honest and committed to his duties, which was borne by the fact that the UT Administrator gave him 9.95 out of 10 points in the December 2018 appraisal.
He gave a detailed break-up of the work carried out under his various charges and how excise collections increased during his time and how there was improvement in the functioning and delivery of the various departments he was in charge of.
Gopinathan said he was "compelled" to give details of his work "to put the specific events of alleged failures/misconduct mentioned in the memorandum in the context of the dedicated efforts put in by me towards efficient and effective public administration".
He also gave detailed replies to each of the accusations of omission and commission.
One of the charges was "Gopinathan visited Kerala in the wake of big flood there to meet the officers and chalk out a plan as to how the UT Administration can help the flood victims. He failed to submit any report on his return from tour".
"I would like to humbly reiterate that, as evident from the above facts and circumstances, I have put in all efforts to deliver as an officer for service of the people of Dadra & Nagar Haveli. However, I regret any shortcomings felt therein and assure that efforts shall be made to improve upon them. Hence, in light of the above facts, I request that the proposal to initiate disciplinary action may kindly be dropped and filed," he wrote.
( With inputs from IANS )