The former Maharashtra Deputy Chief Minister said he would seek "natural justice" and would challenge the decision in the city civil court.
"If Vilasrao Deshmukh got justice, why not me," he asked.
"There is no impartial election taking place here. I demand that MCA President's election should be set aside. The court should order that it should be held again," Munde said.
The leader's application was rejected by the election officer on Saturday as the address on his electoral registration was Beed after which he filed an appeal which has now been turned down.
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According to MCA rules, only a Mumbai resident can become a governing member of the cricketing body.
He said that MCA has become "fiefdom" of Pawar. There is monopoly (of Pawar). Even cricketers are not happy there," he said.
"I will file a separate PIL for that. There is a law in MCA that one cannot contest MCA elections for the fourth term without a gap four years. I am the member and will ask questions during MCA's general body meeting," he said.
In 2011, Vilasrao's nomination for top MCA post was challenged on the ground that he was not a permanent resident of Mumbai but of Babhaigaon in Latur district. However, the returning officer had allowed the nomination on the basis of the details of his residence given in his passport (showing him a Mumbai resident).