Shetty lost to MCA treasurer Savant by five votes to 10 in the battle to take over the reins of the MCA as its stop-gap president in place of Vilasrao Deshmukh who died earlier this month.
"I am sending a letter to MCA that I am stepping down as the vice president. I have lost the confidence of the managing committee," Prof Shetty told PTI after his loss.
Shetty was referring to his belief that some members of the managing committee who were close to him had voted against him in the secret ballot.
Shetty's departure from MCA will put an end to his connection with the association after a quarter century during which time he progressively rose from being a committee member to its joint secretary, treasurer and vice president.
Shetty manned the dual role as the elected member of the MCA and as the paid employee of the BCCI over the last few years with aplomb.
He was also the tournament director of the 2011 ICC World Cup, held successfully in the sub continent with the final held at the MCA's Wankhede Stadium.
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As per the MCA regulations, the 17-member managing committee elected the interim president following the death of incumbent Deshmukh who passed away in Chennai ten days ago.
Savant, the MCA treasurer, will remain as president of the association till the next elections scheduled for April, 2013.