Mr Rao had retired in January 2016 and was later was appointed to head the state-run body that has a budget of over 170 crore rupees and looks after the concerns of the Brahmin community in the state.
Over the last few months, the soft-spoken bureaucrat shared posts including those that called the Chief Minister casteist as well as criticised tax concessions given to a movie - 'Gautamiputra Satakarni'- that stars Mr Naidu's brother-in-law N Balakrishna as well as Baahubali.
Another post that the official had shared accused Mr Naidu of having a hand in getting a cartoon critical of his father-in-law NT Rama Rao published in a popular Telugu newspaper 23 years ago. NT Rama Rao was dethroned in a palace coup by Chandrababu Naidu in 1995 and it has been a touchy topic with the TDP chief.
The government said it hadn't been able to figure why Mr Rao took to social media to vent.
"We don't know why IYR Krishna Rao shared these kinds of posts when he was part of the government... Mr Chandrababu Naidu always had great regard for him,'' Parakala Prabhakar, media adviser to the Naidu government said.
"I have posted and commented from (US President) Donald Trump to crops in Srikakulam (district of the state). I also posted that tax concessions on 'Gautamiputra Satakarni' and extra shows for Baahubali is not right. They have attacked me for that,'' Mr Rao said.
He also admitted that he had felt "slighted on multiple occasions" by the government and had been trying to meet the Chief Minister for the last six months. "If the government had asked me for an explanation on my posts, I would most certainly have explained," he said, suggesting people should be more tolerant of "political satire".
Demands for booting out the official from the post had grown louder for some time now.
Bonda Umamaheswara Rao, a legislator from Vijayawada, said Krishna Rao could not continue in a government position after posting defamatory material about the Chief Minister. "Why is he expressing unhappiness over various issues even though he enjoyed good relations with Chandrababu Naidu?" the legislator said.
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