In his complaint filed before the Metropolitan Magistrate Court at Esplanade, Sayyed Abbaz, a Mumbai citizen, said he and his community felt offended by such "derogatory" remarks and a wrong message is put out to the society.
Abbaz requested that a case be registered against Rahul for promoting hatred among religions.
"I belong to Muslim community and have been teased by non-Muslims and various policemen that (whether) my community people are in contact with ISI or not," said Abbaz in his complaint filed through his lawyer Ejaz Naqvi.
"Gandhi also tried to create a communal divide and communal hatred (among) major religions in India", he alleged.
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Abbaz alleged that he had approached Colaba police to register a case against Rahul but was refused.
The matter is likely to come up for hearing on November 11.
In a public rally in Indore, Rahul had claimed that intelligence agencies in Pakistan were approaching some victims of the Muzaffarnagar riots to lure them into terrorism.
Rahul's statement in which he cited an intelligence input was widely criticised by BJP and other parties.