The faculty of the All India Institute of Medical Sciences on Thursday accused Health Minister Anbumani Ramadoss of undermining the dignity of the institute.
Ramadoss, who is in Chennai, said the institute's administration had gone into a slumber and become ineffective.
He also said Director P Venugopal was free to resign.
"He [Venugopal] doesn't need to go around lobbying," Ramadoss said.
The trouble began after Officer on Special Duty to the Minister D S Moorthy sought the replacement of the AIIMS public relations officer, sub-dean and senior financial advisor, and recommended action against its medical superintendent without taking Venugopal into confidence.
The faculty demanded Ramadoss's removal from the post of president of the institute.
Venugopal told a press conference, "During the last two years there has been a systematic undermining of the institute and the authority of the director. I am disturbed with the humiliation to the respect and dignity of my faculty, officers, residents, students and staff.
"It is my duty to ensure that legitimate interests of the institute and its functionaries are maintained... in case I fail in my duties to deliver as the director and to prevent the destruction of dignity and autonomy of AIIMS, I would not hesitate in leaving the chair."
The Faculty Association said in a statement that Ramadoss has been personally targeting AIIMS and victimising faculty members and other staff for vested interest.
'We demand his immediate removal as President of AIIMS,' the statement said.
Ramadoss denied these charges and said: "We are trying to revive research activities at the institute. It was instituted for research purposes but not much research was happening there," he said.
Ramadoss pointed out that he had got a budget of Rs 500 crore for the institute and completed some of its long- pending projects.
"Institute like AIIMS need to function more efficiently and the ministry is trying to generate more funds for it and is working towards improving hospital care at the institute," he said.
Moorthy had on June 9 issued orders to replace the AIIMS sub-dean and PRO, faculty members claimed.