Known for its controversial stance on a host of issues including the allegations against Islamic preacher Zakir Naik, the SEC's decision came when AIMIM is gearing up to put up a good showing in the Greater Brihanmumbai Municipal Corporation polls, due early next year.
The parties which lost their registration also include RPI-Khobragade faction, led by Uttam Khobragade and UP-based Peace Party.
So far, 359 political parties have been registered with the Commission out of which 17 are recognised parties, he said.
Notices were served to 326 parties for failure to submit necessary documents, Saharia said.
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Despite sending reminders to them and extending the deadline on request of some of them, they had failed to submit required documents, he said.
"If the parties want to contest elections in Maharashtra, they have to register," Saharia said.
For long a Hyderabad-based party, AIMIM expanded its influence to Maharashtra in 2014 Assembly polls by winning two seats, one in Mumbai and another in Aurangabad.
"We received a notice from the SEC four months ago and we had clearly replied to it. Yet, they deregistered us. We will appeal against the decision to the higher authority," Pathan, who represents Byculla Assembly seat in the state Assembly, said.
A press release issued by the party's group leader in Maharashtra Assembly and Aurangabad MLA Imtiaz Jaleel said on receiving the SEC notice a party team from Hyderabad had gone to the Commission office in Mumbai and completed all the formalities as required by it including submission of IT returns.
AIMIM respects the independent nature of the Election Commission and fully honour their decision to bring transparency in the election process. For AIMIM the upcoming local body elections are very crucial and the party will contest with full force, the release said.