Kumble, who has been associated with the Indian Premier League franchise since January 2013, has decided to pursue other opportunities in sports and cricket.
His decision follows a BCCI crackdown on conflict of interest in the board. Earlier in the month, India team director Ravi Shastri was removed from the IPL Governing Council while selector Roger Binny, whose son Stuart is a member of the national team, was asked to leave.
Around the same time, Sourav Ganguly replaced Kumble as the BCCI Technical Committee chief.
"Mumbai Indians is grateful to Anil Kumble, India's highest wicket taker in both Tests and one days for his contribution in strengthening the Mumbai Indians Franchisee. In his first year as the Mentor, Mumbai Indians won the IPL and the Champions League in 2013. Mumbai Indians won the IPL once again in 2015," said the team in a statement.
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Kumble, on his part, said, "I sign off with the obvious satisfaction of moulding a set of brilliant individuals to a high performing unit. Over the 3 years, MI met unprecedented success winning the IPL twice and the Champions League once. Winning both trophies in the same year (2013) being our crowning glory.
"The players and my support team (coaching and non- coaching staff) have been an admirable bunch and were a joy to work with. Finally, I thank the MI fans for their constant support," added the former India captain.