Although the organisation wanted to take out a protest march from Byculla to Taj Hotel, the police did not grant permission to them to do so.
Thereafter, members of the organisation sat outside their office carrying banners with 'Netanyahu go back' written on them and raised slogans in protest.
The outfit, which represents Barelvi Sunni Muslims, alleged that Netanyahu's visit to the city was a "publicity stunt".
Netanyahu visited the Chabad House, or the Nariman House in the metropolis, after meeting 11-year-old Moshe Holtzberg, whose father Rabbi Gavriel Holtzberg and mother Rivka were killed along with six others there during the 26/11 terror attacks.
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He also criticised the police for not allowing his organisation to hold a "peaceful" protest.
"Along with over 300 Islamic scholars, we were proceeding to Taj Hotel, where Netanyahu is staying, and wanted to wave black flags at him. But we were not allowed to do so in the name of security. But we will continue protesting, till he is there in Mumbai," Noorie said.