In his resignation letter to Information and Broadcasting Minister Rajyavardhan Singh Rathore, he said that due to his commitment to the show he will be stationed in the US for "nearly nine months between 2018 and 2019 and then for a similar period for a minimum of three years more".
"Given this assignment, it would not be fair to me, the students and management team, for me to hold a position of such responsibility and accountability, without being actively involved in the operations," he said in his resignation letter.
His resignation letter has been accepted by Rathore, who thanked Kher for his services to the premier institute, sources said.
Kher had replaced Gajendra Chauhan, who had a controversial tenure, as the head of the Pune-based institute in October last year.
(With inputs from agencies.)