Mistry received 95 votes, while Harmalkar received 185, with one vote being deemed invalid.
Abhay Hadap, who was elected earlier this month, is now the secretary of the cricket governing body, and Harmalkar takes over from him in the Apex Council.
Sachin Tendulkar supported Suraj Samat, who was defeated by Hadap.
Since its president Amol Kale passed away in June, the MCA has held three elections in recent months.
Ajinkya Naik, a former secretary, defeated vice president Sanjay Naik in July to take the presidency.
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According to a statement released by MCA president Ajinkya Naik, “the maidan, office, school, and college club secretaries have demonstrated their positive influence in securing this election win once again.”
“We are still dedicated to the expansion and improvement of Mumbai cricket, as this is our team’s third straight win. In this election, cricket players of both genders showed their support,” he continued.
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